Is my cat submissive?

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Here's the deal... I have a 3 year old male cat who has been neutered. Recently, we have had another male stray coming into the house who has not been neutered. We did try to get a micro chip cat flat but unfortunately it wouldn't fit in the window panel where it needed to go so the only one we could get was a standard flap. Now we have this new cat in and out all day. The 2 seem to get on which is odd given our cat seems to chase any other cats away. Last night I saw the stray come in and eat his food... and he just watched and did nothing. I'm wondering whether he is intimidated by this other cat or whether they genuinely get on? Either way, I think we're going to have to adopt the stray....