I thought mp4tools also was able to either burn in or add as separate track srt subtitles. If not in the regular version, have you tried the beta which has been totally re-written to use ffmeg instead of mplayer?
The (textual) sub support of the non-beta version was awful - it messed up everything with files with more than one sub track.
The new beta indeed rocks. It not only retains the subs (all of them), but is also, in average, two times faster than the prev. version and I've never encountered crashes - unlike with the old version.
It's still 40...100% slower than Subler, though and, in addition, I've found some direct BR rips it just couldn't remux, as opposed to the prev. version. Two examples: the Iron Sky trailer from the official Finnish BR disc and the behind the scenes from the same BR disc. These couldn't be converted: the app created a useless, 4 kByte-file in 1-2 second, independent of audio selection.
The main movie from the disc was remuxed 2 times faster than in the prev. version.