Any mechanic worth going to will not care about mods, if you are just looking for regular maintenance or to address a specific problem.
If it's a drivability, performance, or emissions issue that is related to mods in conjunction with a flash tune, you will have to see a tuner. A regular mechanic is only going to be able to diagnose physical mechanical and electrical problems and check that a sensor or something is either within factory spec or otherwise reasonable, but they aren't in the business of custom ECU programming.