Hello and welcome to BW forums
I also had a LO who didn't eat very much but he gained weight well and stuck within his centile lines for growth.
If your LO is gaining weight well, keeping to his growth centiles and the reflux symptoms are managed with the meds then I wouldn't be too concerned about the actual amount he is taking at each feed. Tracy did say in the BW books that some babies just can't manage the 4hrly E until more like 6 months and when solids are introduced. It is still possible to use the EASY routine and BW methods/ethos on parenting without forcing your LO to move to 4hrly E times. The routines in the books are guidance only and the whole BW ethos is to adapt to your LOs needs to make an appropriate routine for the individual.
In terms of reflux, if it is only that he needs to eat with the shorter time between but can settle for naps well enough and his sleep is not effected by the reflux then I'd consider it well enough managed as it stands. If though his sleep is disturbed and he appears to be in pain or disturbed by the reflux then I'd look into what else can be done to help control it. It's quite common for refluxers to need to eat little and often.
My DS stayed on 3hrly E until 6 months when I started BLW, having solids between the milk feeds helped him to shift his milk feeds naturally.
If E is at 3hrs (or you can do 3.5hrs if your LO is happy with this) then the EAS routine obviously changes a little. LO might need the longer A time to be able to nap well but still need the shorter E time. It's okay, you just track the times and look for a suitable routine for his needs.
We can help with this if you like?