Please let me use my software how I want to. If my choices in how I use my software cause it to break or slow down, that should be my decision whether that is acceptable, not yours.
You could also send the plugin some in-memory-only version of my frontmatter, leaving what I wrote untouched but still sending them your idealized version.
At the very least give me some setting/option/preference to preserve this stuff, please. To me, it’s unacceptable for you to destroy my data just to allow some hypothetical 3rd-party plugin dev to have an easier time reading something I didn’t write.