Although warnings are not shown for math formulas at a paragraph level (T225118), they seem to still be counted when deciding to prevent the publication of the article.
A user in this comment reports problems when translating the article "Prime omega function" from English to French.
I tried to reproduce the scenario by modifying text in the initial paragraph to avoid the 99% limit on unmodified MT for the whole document, and kept adding paragraphs and publishing the translation until the tool prevented me from publishing.
According to the current translation limits the publishing error should happen when reaching 50 paragraphs with a warning. However, in the image below you could check that only 25 paragraphs have a warning, while many other paragraphs consisting of a math formula do not show any warning. Math seems to still be computed in some way:
(This is a long full-page screenshot, download and open locally for a better view)