Is this something we should change in future uploads *to* CTAN
You don't have to change anything if you don't want. I'll fix the
location in TL after the release.
In principle, I do think macros/luatex/latex would be a more appropriate
place on CTAN than support (which is something you would specify when
you upload), because lyluatex does not include user-visible command-line
executables, just Lua code, if I'm understanding correctly. Packages
with executables is usually what the CTAN:support directory is used
for. But of course there are no 100% rules, so leaving it alone is fine
by me. --best, karl.