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Right now it's not really a problem if you directly modified files in /system (or /vendor) as Onyx is still putting out unconditional updates. When they become incremental (i.e. much smaller than 1 GB) is when that will change. At some point you may need to restore /system and/or /vendor to do an update.
boot.img is monolithic, so it will either get replaced or not, same for recovery.
I've actually gotten away from Magisk, but that's irrelevent.
I've been doing updates using direct download, decrypting to zip and using a USB flash drive and a custom recovery (just because I can). I've disabled too much Onyx stuff already.
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