Something to point out from earlier boot:
e[1;55re[54;1H[0002.228] I> enabling 'vdd-hdmi-5v0' regulator
e[1;54re[54;1H
e[1;55re[54;1H[0002.234] I> regulator 'vdd-hdmi-5v0' already enabled
e[1;54re[54;1H
e[1;55re[54;1H[0002.234] E> tegrabl_display_init_regulator: hdmi cable is not connected
e[1;54re[54;1H
e[1;55re[54;1H[0002.235] E> tegrabl_display_get_pdata, failed to parse dtb settings
e[1;54re[54;1H
e[1;55re[54;1H[0002.241] E> invalid display type
e[1;54re[54;1H
e[1;55re[54;1H[0002.247] E> invalid display type
e[1;54re[54;1H
e[1;55re[54;1H[0002.248] E> cannot find any other nvdisp nodes
e[1;54re[54;1H
e[1;55re[54;1H[0002.248] E> no valid display unit config found in dtb
e[1;54re[54;1H
e[1;55re[54;1H[0002.253] W> display init failed
Are you operating without HDMI (and can you give details on anything which may be special or unusual about the monitor)? This isn’t in itself an issue, but if you have a monitor connected and still see this, then the i2c query is failing and may be a side effect of hardware failure (normally this is just a device tree or monitor issue, but for your case perhaps it is more).
Later, as the kernel starts, this is what I see for the kernel command line:
e[1;55re[54;1H[ 0.000000] Linux version 4.9.140-tegra (buildbrain@mobile-u64-2988) (gcc version 7.3.1 20180425 [linaro-7.3-2018.05 revision d29120a424ecfbc167ef90065c0eeb7f91977701] (Linaro GCC 7.3-2018.05) ) #1 SMPe[54;204H e[54;204HPe[54;204HRe[54;204HEe[54;204HEe[54;204HMe[54;204HPe[54;204HTe[54;204H e[54;204HWe[54;204Hee[54;204Hde[54;204H e[54;204HMe[54;204Hae[54;204Hre[54;204H e[54;204H1e[54;204H3e[54;204H e[54;204H0e[54;204H0e[54;204H:e[54;204H3e[54;204H0e[54;204H:e[54;204H1e[54;204H1e[54;204H e[54;204HPe[54;204HDe[54;204HTe[54;204H e[54;204H2e[54;204H0e[54;204H1e[54;204H9e[54;204H
There are a lot of characters there which may or may not be something the kernel understands. After the unit boots, what do you see from:
cat /proc/cmdline
(if those are just ansi escape sequences, then it is likely the terminal itself putting those characters out)
The odd characters could simply be from applications reading the logs not understanding the character set/encoding, but it is worth examining.
Later on I see more i2c errors, not necessarily associated with the display (but perhaps).
For the Gemalto Key, did you have to install any drivers? User space software? i2c and USB are unrelated, except perhaps if the USB is talking to a custom i2c device.
On the serial console, with just a mouse or keyboard installed, what do you see from “lsusb” and “lsusb -t”?