I've played in a trio for years. I've never really found it a problem at all, in fact it's quite liberating. I mostly play standard bass lines, but every now and then we might have to rearrange slightly to get some key riffs in e.g. on Witch Queen of New Orleans by Redbone I play the rhythm guitar riff as the guitarist sings that one making it difficult for him to get the timing rock steady.
As regards sonic space, I have no constraints and can play with pretty much any eq I like. The key thing is the standard bass role of locking in with the drummer, even if he goes off on one as well. You are the main anchor.