This functionality is only available on kernel 3.10.y so far.
On kernel 4.9.y and 4.14.y, we're planning to include this HDMI PHY tuning options in hdmi kernel driver.
Once it's done, the version will be specified here.

If your HDMI TV or monitor is too sensitive and does not display correctly, it is worth it to adjust the HDMI PHY on the XU3/XU4.
To use this feature, the Kernel version must be be 3.10.82-47 or higher.

This portion of the default boot.ini file comes with the 3.10.82-47 update.

#------------------------------------------------------------------------------
#
# HDMI-PHY Parameter Control
#
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
#
#  TMDS data amplitude control.
#
#------------------------------------------------------------------------------
#
#  1LSB corresponds to 20 mVdiff amplitude level.
#  tx_amp_lvl : 0 = 760 mVdiff(Min), 31 = 1380 mVdiff(Max)
#
#  Hardkernel default hdmi_tx_amp_lvl = 31(1380 mVdiff);
#------------------------------------------------------------------------------
setenv hdmi_tx_amp_lvl  "31"
 
#------------------------------------------------------------------------------
#
#  TMDS data amplitude fine control for each channel.
#
#------------------------------------------------------------------------------
#
#  1LSB corresponds to 20 mVdiff amplitude level.
#  tx_lvl : 0 = 0 mVdiff(Min), 3 = 60 mVdiff(Max)
#
#  Hardkernel default
#      hdmi_tx_lvl_ch0 = 3, hdmi_tx_lvl_ch1 = 3, hdmi_tx_lvl_ch2 = 3,
#------------------------------------------------------------------------------
setenv hdmi_tx_lvl_ch0      "3"
setenv hdmi_tx_lvl_ch1      "3"
setenv hdmi_tx_lvl_ch2      "3"
 
#------------------------------------------------------------------------------
#
#  TMDS data pre-emphasis level control.
#
#------------------------------------------------------------------------------
#
#  1LSB corresponds to -0.45dB emphasis level except for 1
#  tx_emp_lvl : 0 = 0 db(Min), 1 = -0.25 db, 2 = 0.7 db, 15 = -7.45 db(Max)
#
#  Hardkernel default hdmi_tx_emp_lvl = 6 (-2.50 db);
#------------------------------------------------------------------------------
setenv hdmi_tx_emp_lvl      "6"
 
#------------------------------------------------------------------------------
#
#  TMDS clock amplitude control.
#
#------------------------------------------------------------------------------
#
#  1LSB corresponds to 20 mVdiff amplitude level.
#  clk_amp_lvl : 0 = 790 mVdiff(Min), 31 = 1410 mVdiff(Max)
#
#  Hardkernel default hdmi_clk_amp_lvl = 31 (1410 mVdiff)
#------------------------------------------------------------------------------
setenv hdmi_clk_amp_lvl     "31"
 
#------------------------------------------------------------------------------
#
#  TMDS data source termination resistor control.
#
#------------------------------------------------------------------------------
#
#  tx_res :
#      0 = Source Termination OFF(Min), 1 = 200 ohm, 2 = 300 ohm, 3 = 120 ohm(Max)
#
#  Hardkernrel default hdmi_tx_res = 0 (Source Termination OFF)
#------------------------------------------------------------------------------
setenv hdmi_tx_res      "0"

If you have a display compatibility issue by HDMI signal strength, try these parameters.

#------------------------------------------------------------------------------
#
# HDMI-PHY Parameter Control
#
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
#
#  TMDS data amplitude control.
#
#------------------------------------------------------------------------------
#
#  1LSB corresponds to 20 mVdiff amplitude level.
#  tx_amp_lvl : 0 = 760 mVdiff(Min), 31 = 1380 mVdiff(Max)
#
#  Hardkernel default hdmi_tx_amp_lvl = 31(1380 mVdiff);
#------------------------------------------------------------------------------
# trial hdmi_tx_amp_lvl = 13(1020 mVdiff);
setenv hdmi_tx_amp_lvl  "13"
 
#------------------------------------------------------------------------------
#
#  TMDS data amplitude fine control for each channel.
#
#------------------------------------------------------------------------------
#
#  1LSB corresponds to 20 mVdiff amplitude level.
#  tx_lvl : 0 = 0 mVdiff(Min), 3 = 60 mVdiff(Max)
#
#  Hardkernel default
#      hdmi_tx_lvl_ch0 = 3, hdmi_tx_lvl_ch1 = 3, hdmi_tx_lvl_ch2 = 3,
#------------------------------------------------------------------------------
setenv hdmi_tx_lvl_ch0      "0"
setenv hdmi_tx_lvl_ch1      "0"
setenv hdmi_tx_lvl_ch2      "0"
#or try below parameters
#setenv hdmi_tx_lvl_ch0      "1"
#setenv hdmi_tx_lvl_ch1      "1"
#setenv hdmi_tx_lvl_ch2      "1"
 
 
#------------------------------------------------------------------------------
#
#  TMDS data pre-emphasis level control.
#
#------------------------------------------------------------------------------
#
#  1LSB corresponds to -0.45dB emphasis level except for 1
#  tx_emp_lvl : 0 = 0 db(Min), 1 = -0.25 db, 2 = 0.7 db, 15 = -7.45 db(Max)
#
#  Hardkernel default hdmi_tx_emp_lvl = 6 (-2.50 db);
#------------------------------------------------------------------------------
setenv hdmi_tx_emp_lvl      "6"
 
#------------------------------------------------------------------------------
#
#  TMDS clock amplitude control.
#
#------------------------------------------------------------------------------
#
#  1LSB corresponds to 20 mVdiff amplitude level.
#  clk_amp_lvl : 0 = 790 mVdiff(Min), 31 = 1410 mVdiff(Max)
#
#  Hardkernel default hdmi_clk_amp_lvl = 31 (1410 mVdiff)
#------------------------------------------------------------------------------
# hdmi_clk_amp_lvl = 16 (1110 mVdiff)
setenv hdmi_clk_amp_lvl     "16"
 
#------------------------------------------------------------------------------
#
#  TMDS data source termination resistor control.
#
#------------------------------------------------------------------------------
#
#  tx_res :
#      0 = Source Termination OFF(Min), 1 = 200 ohm, 2 = 300 ohm, 3 = 120 ohm(Max)
#
#  Hardkernrel default hdmi_tx_res = 0 (Source Termination OFF)
#------------------------------------------------------------------------------
# 200ohm termination
setenv hdmi_tx_res      "1"
#------------------------------------------------------------------------------