system
Given the following post, respond as if you're commenting on Reddit:
human
[General] I'm worried that my space empire is actually interleaved with other species' realms (methane breathers, solar dwellers, etc). How can I realistically protect my so-called "borders"?

In terms of them wanting my planets we should be pretty okay ... I don't want to live on Jupiter, for example.  But eventually there'll be contention over asteroid belt mining, or my Navy will get too jittery watching incomprehensible alien vessels flit about and simply blow them away.
gpt
You either make the call to spend resources defending planets that are useless to you out of some sort of xenophobia, or you realize that interleaved borders aren't a problem.  
In the latter case, you keep the lines of communication open, negotiate ahead of time, and in the worst case just defend the resources you care about rather than defending everything.