Okay, that helps clarify things!

Going back and re-reading your post with that information in mind...
Re: the DF. Some people don't do it...I think it's your choice and you know your LO best! It sounds like you'd be able to recognize very quickly if she was starting to consume more and more calories at night thereby disrupting her daytime eating habits. So, as long as you don't mind her waking every now and then to feed her (should only be once, max twice a night if it's hunger, with a quick resettle (like 5-10 mins)), you could keep things as they are.
If you would like to implement a DF, I've found that giving a bottle works best. I tried DFing with a breastfeed, and DS just fell asleep even faster and wouldn't suck--totally counterproductive. You actually don't wake up your LO to do a DF, nor do you burp them (unless you feel you really need to--most are so relaxed bc they're sleeping that they don't need it). Yes, you get them out of bed for the DF. I have a chair that I sit in right next to DS's crib, but have also taken him into another room (didn't work too well, tbh). You want to treat the DF like a full feed, which is why it normally happens a few hours after their last (bedtime) feed. For example, my DS is on a 4h eating schedule. If he gets his bedtime bottle at 7, then I do the DF at 11 and fix him what he normally eats during the day.
When she wakes up at night, what is she acting like? Is she crying a tired cry or a pain cry (does your LO have reflux)? Is she babbling or cooing? Grunting (like passing gas)?
It still could be that she needs more A time. I'm not saying this with 100% certainty, but you might just try it. At 3.5 months, DS was up to at least 1.5h. You know your baby best though and see how she handles this. Out of curiosity, do you know her temperament (angel, textbook, etc.)? That might give further insight

How are naps during the day? You mentioned how the first one was, but how are the rest? Do you think you could post what yesterday looked like in the EAS format (it's just easier to read through and spot things)?
The reason I ask about her naps is that they can be indicative of her A time needs as well. What might be happening is that her first A time is too short, so she wakes up at 45 min (at the end of a sleep cycle), and feels rested enough to be up again and won't go back to sleep. This is an UT or undertired nap.
From here, what then can happen is that it goes into an OT (overtired) cycle...she stays up too longer after that first nap and then has OT naps for the rest of the day, and the OT exhibits itself in the night. And then it starts all over again the next day...
If her A time actually is just right for her, then something to consider is really tackling those naps and work on extending them. For the first 3 months, LOs are working on their night sleep; but from months 3-6, they're working on their day sleep. This is when most nap problems appear. Have you tried any preemptive nap extending methods (like wake to sleep, holding through the jolts, shield eyes, darkening room)? What does your naptime wind down routine look like?
Sooo, let's see where we can go from here!
