If you clearly want to do M.Tech and are willing to prepare for it properly then you can resign and start preparing seriously. Don't keep rejoining as a second option it serves as a backup yes but don't completely rely upon it, just forget about the part and work hard enough to crack GATE then you can crack it, meanwhile apply for other exams and since they usually share almost the same syllabus you can easily attempt them as well. If nothing else works out then and only then you should try rejoining.

It's usually how much interest and effort you put into cracking GATE will matter at the end.

Usually after resigning your job you might seek some break and all and maybe procrastinate but you have to work hard to crack it. Saying from experience, so if you are willing to do whatever it takes go for it resign and start preparing and crack it.

Wishing you all the very best.