There are various possible reasons why you may be trapping excessive food under your All-on-4 denture. If your denture is an acrylic one, it may have a concave area underneath. If this is the case, it can be relatively simple for your dentist to reshape that so it is flat (or even convex) instead. While this many not fully eliminate trapping, it should minimize the issue so that it is manageable with good hygiene.
At my practice, I use digital smile design, mock ups, and provisionals as safeguards to ensure the patient gets the chance to try their new smile before it is permanently cemented on. Though techically it IS possible to reshape a crown after it is placed, it all depends on the material used and also on how much room was left on the porcelain for reshaping. Typically, if a patient does not like either the color or shape of a crown AFTER it is already permanently cemented, it will essentially need to be redone.
The decision to replace a back tooth or not resides with you but the doctor's recommendation is based on his assessment of your chewing function, occlusion, and other factors. To avoid excessive pressure and wear on opposing sides of the missing teeth, you'd want to preserve balance. Whatever you decide, a bone graft is highly recommended at the site of extraction to preserve the ridge there and avoid excessive bone loss.
Prior to placing the implant, your dentist would have taken a CT scan which would enable him to properly examine your bone mass and plan on where implants could most successfully be placed. Besides assessing where your bone is sturdiest, your dentist would also plan on the angle in which the implant must be placed. If your bone is at an angle, the implant also should be. That should not create a problem for you. The dentist will just need to ensure the crown atop the implant compensates for the angulation. I would urge having that crown/implant re-evaluated and adjusted.
If your dentist knows your case well he/she would have recommended the solution that is most viable for your needs. If you are unsure, you should get a second opinion before placing that implant. Instead, you might have considered having bone grafted in the area that is thinned. This typically rebuilds bone height to prepare for a regular-sized implant. Since mini implants are a lot smaller, in my view, there is a limit to the force they could withstand which could result in a shorter lifespan.
