Visa run in 2 months, Where to ?

My guess is that they will not issue overstay fines while travel restrictions are in place.Everyone will probably receive a waiver while immigration offices are closed and you can then get whatever remain of a one month extension.

But visa runs are implicitly not allowed as immigration does not consider long-term residence as "tourism". One is asked to apply to the MM2H program for that and it's only for those who can demonstrate the wealth, health, and lack of police record that they expect.

Right now many countries are not allowing people back unless they can demonstrate they are permanent residents. "Transit through", may be allowed in some places (Singapore ended even THAT) but that would not allow you to return to Malaysia. You'd have an "exit" stamp but no entry stamp into the other country. You'd have no boarding-pass to get on a return flight either.

Ever see "The Terminal" with Tom Hanks?

If Thailand, Indonesia or Singapore are still placing entry restrictions then there may very well be no place you can make a run to...unless you want to quarantine in place for 2 weeks. And the same rule may exist when you return.

Indonesia is letting everyone stay for an extra month, but people need to visit immigration to get the extension stamp. I would guess that Malaysia would be doing the same since as mentioned above countries are blocking entry and flights are becoming very limited. I would check with immigration. Perhaps there is something on their website.