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I just wanted to note that after experimenting further with this, it seems that the number of distinct paths was the prime culprit, rather than the file size. I’ve been working with ~10 MB files that have about 1/100th the number of paths and there are no issues when pausing. (Basically, instead of using many short paths, I made sure to join them into long paths with multiple vertices.)
Since pausing is done by updating the SVG itself, I wonder if there is perhaps some inefficient behavior in the Inkscape extension around finding/updating individual paths?