I think you're absolutely doing the right thing by not going in. If it escalates or if she cries-cries then definitely go in. But if she's just making noise as you say, then leave her alone. Sounds like she's doing great with independent sleep already, good for you!
Looking at your routine though, I wonder if maybe it would be time to lengthen her A time a bit. It looks to me like she has an hour or less at a time, and I think around 3 mo. she should be able to do a bit more. She should go down to 3 naps a day soon too - she might be getting a bit too much day sleep right now in that transition period, which could be contributing to the night noise.