I'm a little confused, because your number 0.25 is the same as mine - perhaps I'm not understanding something (which is very likely!).
The manual says to measure the cylinder at bottom, mid and top on x and y axis. Rebore the cylinder if beyond Serviceable Limit (58.60mm) at any point. Standard oversizes are 0.25 ,0.50 etc. etc.
It then says to measure the piston and replace if beyond the Serviceable Limit (58.35mm).
So, let's say the cylinder is at 58.55mm and the piston is at 58.45mm - both worn, but within their respective limits. This would result in a clearance of 0.10mm
As the extreme example, the cylinder would be at 58.60 and the piston at 58.35. Both right at their serviceable limits, resulting in a clearance of 0.25mm
Considering the initial maximum clearance of 0.04mm, I agree, 0.25mm sounds like an awful lot.
Bottom line is I agreed to this addtional work with my mechanic because he said an additional 3 hours labour to take the top end off and then put it all back together after machining work was completed. This also means they will re-tune the bike when back together, which is what I was originally there for. They already did 5 hours labour on the bike initially rebuilding the carbs, replacing points/condensors, doing the timing and tappets and then trying to synch the carbs and get things going. Another 3 hours labour isn't much $ wise, and I'd have to buy all these parts and have the machining work done regardless.
I think for the extra cost of 3 new pistons and boring vs. honing, I'm best off boring to the next oversize based on the maximum cylinder clearance measured in any of the 4 cylinders. Then at least I won't have any issues for years and years to come (with the cylinders anyhow).