I'm not an expert, However I do dable a little in engine work.
If you mean bore the cylinder before or after porting. I would say after.
The head will need to be modified depending on over bore size and type of port work and any cylinder modifacation.
The builder will need the head to dial in the engine.
I'm surprised the builder does not need the whole engine unless it's a generic port job. I mean by this it's a basic clean up with minor mods where there is built in clearance variables.
One must have a clear cut P L A N for the engine before a builder start moding. If not it's just a generic job.
Trust who you send it to and discuss all the parts you plan on using and the fuel type,rpm ect. No two engines are the same. Heck you just change type of pistons or bore it after the fact and not maitian the enige builders ring caps top to bottom it could lead to failure. I see this a lot in piston pics where the top ring looses seal and blowes past the second ring siezing it up. The ring gaps play a part in pressure sealing and ring flutter in the land area between rings. This is how just one minor thing can upset a build, now compound that with bolt on item changes or rpm changes or fuel. In a high preformance build all of the P L A N must be maintaied or a recalucation must be done. Gaskets sets can vary mfg to mfg. One must have the data to replace with out upsetting the P L A N.