You can't disable the serial console entirely, what you can do is set the kernel command line to quiet (but this will also hide a lot of useful output). I would recommend using specific test job definitions which only do a boot test when running with a quiet kernel and also ensure that the actual kernel image correctly boots (without quiet) before running the measurement test job. Equally, if what you are testing is kernel boot time, be aware that you should only use ramdisk test jobs and use as small a ramdisk as possible so that the INIT stage happens with as little fuss as possible. As it's only a kernel boot test, for example, you do not want INIT trying to get a DHCP address when what you want is a time measurement. Different test jobs for different use cases. You certainly don't want the extra time delay of communicating with NFS - that delay is not predictable and the rest of INIT will be affected if the LAN is slow. Try to get a cusomised ramdisk which (as near as possible) always takes the same amount of time to run INIT.
The timing also depends on the DUT and the kernel configuration. If the kernel is very noisy and produces a lot of debug to the console, it can take some time for the DUT to send that information and LAVA cannot do any measurements until the output has been sent from the DUT over serial. It is lava-run which is doing the timing, on the worker, so it is as close as we can get to the DUT.
The final option is to write a custom kernel module / kernel configuration which measures and records the kernel boot time independently of the serial port. Then access that value after boot from a Lava Test Shell. This gives you full control over whether you are measuring only the kernel boot time or kernel + INIT.