Well I would count the 3hrs from the beginning of the feed to the beginning of the next feed so counting from 6.30am I would (as you are) count the next 3hrly feed to be 9.30am. However, unless there is a clear weight gain problem and you have been told by your paediatrician to ensure you feed every 3hrs and not any further apart, I would just let her sleep. 4hrs sounds a long time but if she is taking a good feed then she is likely fine to go that long. Many babies who are kept in hospital after birth are put automatically onto a 4hrly E routine. I would trust that if she is sleeping she is not yet hungry and just let her have her nap, feed on waking. If some of the feed times are 4hrs and others are 3hrs I think that's fine.
At 3 wks old mine was still on 2 to 2hr 30 E and I began to slowly move him towards 3hrs at about 5 wks old - all different!
I probably wouldn't let her sleep past 3hrs in one go in the day though.
Do you need some BF support? There can be tips for increasing supply so that top ups of formula are not needed.