Yes you can do custom resolutions, it’s on the top right. You can chose source, scale to a specific res, or fix H/W and it’ll calculate the other.
There’s a section for Add subtitles as well. You’d have to play around with it some, I don’t know all the ins and outs.
Usually what I’ll do is I’ll recombine the folders into an iso file using mkisofs and then keep the ISO as it keeps all the menus and everything in tact. Later if you want, you can run that ISO through MakeMKV and just rip out an MKV of the main title through. But since I have enough disc space I just rip all my DVDs and BDs to straight ISOs to keep all the menus and extras in tact for later.