yes -- it's a well known problem. applications, which wont to support 8bit and 10bit h.264 support, have to utillize two variants of libx264 and switch between them.
well -- it's a comprehensible decision, but i'm not sure, if it's really a wise choice in practice?
the use of 10bit in h.264 isn't very well supported in most software and hardware decoding solutions. it's usually much more advisable, to use h.265 or VP9 if you really need 10bit bitdepth. but even in serious movie making it's often very handy, if you are able to produce deliveries in common and compatible 8bit h.264.
export in conventional intermediate formats (prores, dnxhr) and transcoding by an extern solution, should be seen as an acceptable workaround. it's anyway necessary in most cases, because natron isn't able to add or preserve the sound tracks right now,
i think, that's more a historic resp. outdated issue. right now simple 8bit 4:2:0 h.264 is available in nearly any browser. from a pragmatic point of view it's simply the lowest common denominator for compatible delivery in html5 right now.
VP9 is a really attractive alternative, but it's unfortunately still not supported in some browsers (in particular on apple devices)