Anyone using PBP3 with hardware timer overflow interrupts for finer control?
Yes, all the time and most times in conjuction with DT-Ints for PBP context save/restore. For periodic/cyclic interrupts using TMR2 (or one of the same type) is nice because you set it up once and then it takes care of itself while with TMR0 and TMR1 for example you need to reload it for the correct period each interrupt.

If the goal is to use timer interrupt for all sorts of delays then it doesn't really matter.

Integration with MPLAB X / Pickit 3
Hate to say it but just forget about it. Apparently it used to kind of work, sort of, about a decade ago but Microchip has moved on an PBP hasn't kept up. I know I've tried several times but always went back to MicroCodeStudio.

PICKit3 on the other hand I still use with the MPLAB IPE software.

/Henrik