Yes it can.
There was at one time, a cast 68.25mm aftermarket piston, but I never used one.
To go larger than a 68mm, with a long rod crankshaft bottom end, you'll need to use the 85/86 style year of piston & then a 3mm spacer plate under the cylinder & two base gaskets to sit the cylinder to the proper height.
Theres a difference, between the old model 85/86 piston & new model 87/88/89, where the wrist pin hole is located in each year piston.
The old 85/86, the wrist pin hole is higher to the crown of the piston than on the 87/88/89 models, then by the new model crank having a 5mm longer rod than the old 85/86 cranks, theres not 5mm difference in the space needs to be taken up under the cylinder from using the old model piston, so only a 3mm spacer plate is needed to take up that difference.
You can bore any year OEM TRX250R cylinder, up to a 69.50mm, but if using the new model crank, the cylinder will need to be spaced to make up the difference of the longer con rod.
If the old model short rod crank used, then no spacing is needed for the 85/86 style piston.
You can also, after the 69.50mm piston is used up, go to the 86 & up YZ250 Yamaha 70.00mm piston.
OEM cylinder, long rod crank & old model piston used, 3mm spacer plate & two base gaskets for it to work.
OEM cylinder, long rod crank & 70.00mm YZ piston used, 2.5mm spacer plate & two base gaskets for these to work.
(Note) if YZ piston is used, attention must be paid to the location of the piston ring end gaps, where those gaps will line up in the cylinder bore, because the ring locating pins in the ring grooves on those pistons, not in the same locations as in a TRX piston. If the cylinder has been heavy ported, it might be possible for the end of a ring or on both rings to catch in a port window, so that needs to be checked very closely.
Neil