ffmpeg is not the issue here, it supports several 444/alpha/lossless codecs quite well, proes is not special in that regard.

Browsers only expose a small subset of codecs that ffmpeg supports. gif and apng are now the most compatible format in browsers for this kind of content.

FourCC of ap4x 'just worked' on IE (I might have installed QuickTime codecs), Safari, and gstreamer with Firefox - it just played in the window (though I did not test alpha channel). I was surprised too ;)