What's the purpose of timing out players for such a huge amount of time like 40 or even more minutes?
I mean for example in classical games I usually abort games when facing players with questionsmarks or weird rating differences. It's just my perspective of view but in my opinion these players have a high chance of being cheaters. I know when they are successfully reported the concerned player will get their points back, but I just don't want to waste my time playing those guys.
Any suggestions to improve the timeout system?
Personally I like the timeout system as it prevents a lot of unwarranted aborts. If one player aborts a paired game, it usually means that the aborting player is at fault and in my experience it is quite annoying when multiple opponents abort against me (I just want to play too!). When I say "at fault", I mean that the aborting player realized that they didn't have the time to play or maybe got cold feet after seeing the pairing, even though they can seek for a pairing that they would be comfortable playing.
In your situation, you could just do a custom seek (rather than quick-pairing) so that you always receive an opponent with a rating that you are comfortable playing (Although that doesn't prevent you from being paired with a provisionally rated player).
I know this didn't address your timeout system question; I don't really know the details of how it works. It sounds like you are abusing the abort button though if you are frequently being timed out.
It's because the first 10-minute timeout didn't make you stop. If you're constantly an asshole to everyone you play (or don't play, as the case may be), the timeouts will become exponentially longer until you stop your abusive behavior: the longest I've heard people complaining about is 2 days. It'll cool down if you go a few weeks without getting banned again, but even then I think the minimum ban time for repeat offenders is longer than the one for a first offense.
The abort function is intended for misclicks and the like, not for filtering opponents (because it unnecessarily wastes other people's time and makes the experience worse for new players).