Most of what I do on the CNC is repetitive set ups or referencing off the same location of the workpiece . With T-track, it is difficult to reliably repeat setups, and I experienced fences moving with some of the forces of machining producing errors.
The hold downs were also higher profile than what I have now.
The dowels are what helps the repeatability on the wasteboard. The dowels hold the fences and wedges, screws hold the fences, but are not required. I also use hold downs, but the head of the screw only projects above the hold down, so it is lower profile than T-bolts in T-track. Low profile connector bolts are also available, but I have not had a need to change out the pan head screws for the lower profile screws. I used 8mm x 30mm fluted dowels, as that's what I had on hand from cabinet making, and they work well for holding the fences and wedges. If I need to double side machine, I place 8mm reference holes which correlate to the offset from the fence on the wasteboard, machine the first side, then inert dowels, flip, and machine side 2.
With homing switches, you can set different WCS coordinates for common setups. I reserve G54 for manual zero, G55 for my typical reference, and G59 for the front extension added on to provide full 33x33 cutting area.
First image is prior to XXL upgrade and previous typical dust shoe design.
Second image XXL upgrade with two wedges holding panel for job
Third image showing layout of alternating 1/4-20 threaded inserts and 8mm dowel holes