Modifications usually involve additions or changes to a guitar. I will define modifications as anything that changes the guitar from its original condition.
Hence, a new custom bone saddle will not classify as a modification because there is no change to the instrument. The old saddle can, in fact, be swapped out and reinserted at any time.
However, adding a bridge saddle pickup, for example, to an acoustic or classical guitar would constitute a modification since new holes will be drilled into the instrument, modifying it from its original condition.
Modifications are a legitimate and common form of improving one’s guitar. However, since modifications will change your guitar (even slightly) from its original form, you should be even more careful to be certain the modification will add value to your instrument. And again, make certain the artisan working on your instrument can do consistent and quality work of the required nature.