Merge mkv and srt before moving the final file

Let’s say I download my .mkv, and after that, a .srt with the related subliminal plugin. http://flexget.com/wiki/Plugins/subliminal

Is it possible to merge the .mkv and .srt into a single file, before moving it elsewhere?

Possible? Yes. Is such a feature available in Flexget? No.

You can rewrite something like https://gist.github.com/altermarkive/4dfc62346796eb1e07f5 into a plugin and create a pull request.

Do you mean that you want to add subtitle(.srt file) to mkv files? If so, you can use Joyoshare Video Joiner. It is very easy to use. Just need to take several steps.
Step 1: Import mkv files to Joyoshare Video Joiner
Step 2: Open the editing tool and add subtitle file to mkv video
Step 3: Export the mkv with .srt files