Also, IS have custom things like mini-bosses and the way of achieving ship-specific augmentation.
Unlike
UltraMantis, is see zero benefit in adjusting Is to latest FTL patch itself - its highly unlikely, that we will see any more official FTL updates. OTOH, CE is constantly updated, and become
de facto unofficial patch. I understand, that some may not like it and OPT out to use vanilla FTL only - well, it's their loss. After all, when someone want to OPT out from, lets say, One and Only (tm) mod manager, he is cut from 99% of mods, too.
Summing it up, for me, basing IS on CE is most effective future-proof way of maintaining IS - especially, that Is author stated limited time availability. Sure, there can exist 32562375532657327856 version of IS to suit different layouts, but who is gonna create it? If someone would be interested in making IS compatible with FTL vanilla latest patch, it would be done dozen of times, already (
UltraMantis, looking at you

). I haven't seen a crowd working on it, though.
So, if we can count only on author for this mod, it's natural for him to spend his time on most effective way (CE integration). As said earlier, it gives big pool of custom enemies, events. balanced weapons, drones, etc, than can be used for IS-specific situations, without re-inventing them from scratch. Not to mention possible help from CE author on smashing bugs, who (author, not bug) is quite active.
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Of course, all after all, it is IS author decision, on what he want his mod to be based. Personally, with "basing on CE" scenario, I see only gains for both end-user, and developer.
/Estel