If the body is repaired outside of an original mold (which is all the time), there is always the chance that there will be some misalignment. I believe I introduced some when I repaired the mounting surface of the driver side headlight on my car. That headlight must be pretty much adjusted to it's limit to get the height correct. I keyed my repair off the remaining pieces but the only way I could make it really right was to make sure that the repair was in the same plane as the mounting surface of the other side. Not easily done in my garage.
If your bonnet was repaired, that could be a cause some alignment issues. I don't think the metal piece will provide you with much adjustment since you have to work with the dimensions of the lock, but there may be some. I think there is more opportunity with the latch slot in the body. You might be able to mount the metal piece and the rubber seal lower so that your bonnet fits more flush.
My bonnet is original and unmolested as is the surrounding body work and the rear edge (by the windshield) is about 1/8" above the body. I described earlier how it is a little skewed so the passenger's side edge toward the rear is a tighter fit than the driver's side edge even though the front is pretty even on each side. It has always been thus. The boot fits worse though I think I can get it to fit a bit better, I don't think I will be able to get it to sit flush the entire length. That's not to say all fit that way or that there are not examples where they fit much better. Such is the state of fit and finish for a Europa TC.
If moving the slot in the body for the lock doesn't work, since we're dealing with fiberglass, it's pretty easy to make changes and with the proper motivation and patience, you might be able to get it to fit much better.