Yuck.
I also ran into similar issue with Hugo, where I'm out of the happy-path. Those short codes didn't work, complex processing of some unique bits of content was easier in Jekyll (but also other script-lang based tools) than it was in tools like Hugo.
Would it apply to all content in a specific layout or only specific bits of a certain layout?
With the way I have it set up with Jekyll, only a specific post gets the audioseek timestamps added to it, because I wouldn't want it to apply to all lists on the site. I also happen to share a single layout for both podcasts and interviews and interview lists shouldn't get processed with audioseek'd timestamps.
With Jekyll this is super easy to pull off because it's only a custom filter. It can be applied to the specific content I want without having to worry about layouts.
Not 100% sure if that would work, but on paper business logic LOC would be about the same and using a regex is the more canonical way to handle this sort of processing anyways.