To get those you take those .sups ripped from the mkv (ripped bluray from makemkv) by using mkvextract which is included in the newest released version 3.1.0 released Jan 19th, 2010 of mkvtoolnix.
about 50MB each...since they're image PGS format.
So then use on windows Optical Character Recognition to convert them to text stream SRT format using
SubRip. In SubRip just play with the parameters till you get it ok then hit spacebar after each correction you make. It's gets smarter as you go so it doesn't take too long once you adjust to OCR'ing them quickly.
Then mux them in your encode with Handbrake adding external SRT subs or do your encode then anytime later remux them in with mkvtoolnix (mkvmerge).
To address your question about forced subs yes they can be added later by remuxing the mkv. Basically in Handbrake or in mkvtoolnix (mkvmerge) you just set the Force flag to enable them. We just need to wait for makemkv to properly recognize them to properly extract them like you mentioned earlier.