I understand what you're saying and the difference between fussing during sleep and real crying. I would soothe straight away for actual crying. For the little sleepy fusses, it's harder to say. Personally, I would not let it go on for 30 mins unless you KNOW that he is asleep and just making sounds in his sleep. However, if he's awake and fussing, it sounds to me like he needs something, even if that something isn't food or a new diapers. He may just need your presence (and at 3 mos, I consider that a true need).
I totally understand wanting your baby to learn to self-soothe. I have read that, generally, babies don't even start to be able to do this until 3-6 mos, so your little guy is just on the earliest side of that. Also, it's not all-or-nothing. When my baby was a newborn, I'd put her down already asleep most of the time, I just tried to put her down awake but sleepy once per night to help her to learn to fall asleep on her own. As she got better at it, it was twice per night. Now, she goes down awake most of the time. Can he ever soothe himself? If so, great! Maybe make it a goal to get him to self-soothe back to sleep once a night (obviously, not a hard and fast rule, but a guideline). If his fussing goes on longer than you'd like -- for me, probably 5 mins -- go to him; but let him try again the next time. This way you know that he can he's getting some practice while you're also getting more sleep since he's not fussing for so long and you can know you're attending to his needs. Gradually, as he gets bigger and more developmentally able to self-soothe, you can let him do it more.