1) I think it'd be easier to just glue a comic reader on top of MAL than rewrite the site to be mal-automation-friendly (besides, MAL is animu-centric and the manga side is an afterthought; the go-to/endrosed-by-batoto mangu database and listing site is Baka-Updates, especially if you read less any less popular works or doujins or webtoons). I guess one could also modify MAL's animu list updater program (is that thing still available?) or some alternative to it to attempt to identify the comic you're reading in your browser and then let you update the chapter number (depending on how it'd fetch data, it'd likely be open to other reader sites too, not just batoto), but that'd be something for MAL/3rd-party-devs to do.
2)"if we haven't touched a manga for a while"
how long is that while?-?
(registered on 2nd of march 2013 so I don't have any entries older than that available)
if anything, you can accidentally overwrite that if you do touch the manga accidentally on a random chapter
(in case you're only aware of the browser-reliant "visited links" feature that changes the colour of visited links - including links to comic chapters - then if you go to my follows, to the right there's a link to the old follows page that displays where you've finished reading. do remember it's literally the last chapter you read/opened though, no advanced reading history available)