As far as I know, they're the same thing - although I know that when my (neutered) boys have done it, it doesn't smell as bad as eg my third last cat who matured rather early and got a few sprays off before he had the trip to the vet. Less hormones etc, I guess. (But others may be able to speak more authoritatively.)
As to what to do? That's real difficult. It sounds like your neutered boy just doesn't like the situation, is anxious; and is trying to make it clear that the house is his territory. (eg he's spraying inside even though (as you've stopped the litter tray) he's using outside to toilet.)
You really need to have the semi-feral cat neutered in my opinion. That's just on general principle. It will cut down on any roaming behaviour and make him calmer - and might lead to less conflict. It will certainly prevent more unwanted kittens from him at any rate.
As to whether it will stop the problems inside the house? I don't know. I think it unlikely, I have to say, now that he's got an established problem with the other cat. (Last year, my current senior boy 'took against' the lodger who was staying with us temporarily - forbye the lodger was quite the most friendly, gentlemanly and courteous neutered tom I've ever known- and started spraying for the first time. They were quarantined in different parts of the house but he still knew and didn't like it one bit.)
You could try Feliway, quarantining, creating a 'safe place' for your current neutered boy and all those good things. I'd be getting the semi-feral boy neutered in any case - and that might work. And put back the litter tray in your current neutered boy's safe place, only allowing him to use it.
Try those (and others might have suggestions) and see how it goes.