well i'll be damned. Must have overlooked it on my end. It's that way for me too; could have sworn it wasn't. It's picard that doesn't have that problem, but that's on prime. Plex doesn't have a problem with it though. Which option from the site above did you use (and how) to fix that timecode?
No issues with subtitles from Prime, just Netflix.
The fix is to use the ‘expand narrow’ feature of subtitlefix.com.
This feature is normally used to alter the timing to synchronise the subtitle with a point at the end of the movie. (To fix subtitles going out of sync).
But, feeding that function with the exact time of the last subtitle and regenerating the file, the resultant subtitle file has the desired HH:MM:SS format, no timings are altered. Took a while to get to the bottom of that issue.