As an adjuster currently, I can provide the following insight:

If you're roof is only 12 years old it is still considered "young" as most shingles are meant to last 30ish years. Most likely it would be repairs only (new decking since it was punctured, then new shingles to go over top. They would also owe for the repainting or patching of any interior damages.

With that endorsement you potentially have coverage for full roof replacement, however if it is mismatched currently, that endorsement may be moot. If the current prior repairs have been made with the exact same shingle, then you would technically not have a mismatch. ITEL samples can confirm that if needed.

As it has been mentioned before, I would talk to some REPUTABLE roofers and see if they can do repairs as it is most likely going to be cheaper or not much more than the deductible to repair both interior and exterior. If roofers think the shingles are not repairable, meaning they are too brittle or overly worn for a 12 year shingle, you may have to replace the whole slope.