I was under the impression Reapers assume the general shape of the last race they turned into techno-orgnic slurry and fed into a Reaper, so all the Reapers look squid like, much like how all humans are humanoid despite having a wide range of heights, weights, races, etc.
If the Reapers are composed of multiple species that went through that process though then the squid thing may well be a shell they're placed into. Not unless humanity was the ONLY species they saw worthy of "uplifting".
Anyways, time for slight topic change.
I like the idea that the squid looking ship is the shell. Because the boss of ME2 was kinda small compared to the rest of them.
If I remember correctly, EDI mentioned that there might have been problems when processing the prothean and thats why they made them into the collectors and not a reaper model