I do think that other dogs (even other neutered males) view an intact, adult male differently. Boomer is no longer a puppy - and other dogs are treating him accordingly.
It sounds like Boomer has been a
very good boy so far - but his patience won't last forever. There may soon come the time that Boomer does not react so passively. It's up to you to keep him out of bad situations - you will have to be much more vigilant.
I don't think this means that you have to avoid other dogs entirely - but you do have to be more aware and more proactive where he is concerned. Consider avoiding areas where you know loose dogs are likely to be, don't
assume other dogs are friendly even if their owners say they are, and think more carefully about the dogs you allow Boomer to socialize with, etc. From your experiences with your other dog - you know that if Boomer keeps having bad experiences, he may decide that it's better to go on the offense with strange dogs before they can attack him. You don't want that, so you'll have to start being more careful.
You can't always control other dogs or, especially, their owners - but you can control the situations you put Boomer in. Now that you know other dogs' reactions towards him might be changing, you can prevent trouble before it happens!