You’re totally right! I tried prefilling a linked record field like you did, instead of a multiple select (which is what I was using before) and I got the same problem you did.
After messing with it, I can provide a little more context to why it’s not working, and why your solution works. It appears that Airtable doesn’t like the space after the comma. So if the prefill options are “Booking Pronovias, Ladybird” (URL encoded) it only accepts the first value. But if they’re written “Booking Pronovias,Ladybird” (URL encoded), then it works. So you should also be able to get it to work like this:
'https://airtable.com/yourformURL?'&'?prefill_projects=" & ENCODE_URL_COMPONENT(SUBSTITUTE(projects,", ",","))
Which is incredibly similar to your solution, but hopefully the context is slightly useful 