Two ways to deal with it.
Change the M208 settings so the max values correspond to the actual physical position when the endstop sensor is triggered
Use G92 to adjust the logical X and/or Y position so the position at the center is correct. Put the G92 in the homing file of X and/or Y with the values needed to obtain the correct center position. One way to do this is have a G1 command at the end of the homing file with the value needed to move to the center and then have a G92 command with 0 as its value to set the logical position to 0, thus matching the physical position. For example in homeX.g you might have: G90 G1 Xnnn G92 X0
Two issues with that:
So instead of saying I can move 250/250 I tell the printer it can only move 250-10/250-15? It's not easy to find the "real" 0/0 when you're homing at some random 250/250 (which in reality could be 248/251 or something else) and then re-iterate from there where your real "0/0" is. Isn't it?
When I use G92 to move the working coordinates I have the issue that it can't pick up the klicky probe after homing again as it's location has change then ...