Since November 2022, foreign nationals holding a Malaysia long term pass and a biometric passport have been able to use the Autogates at KLIA and KLIA2: https://www.klia2.info/news/2022/autogate-system-at-klia-extended-to-long-term-visit-pass-holders-from-nov-15/
Using the Autogates as an LTSVP holder
As an LTSVP holder, before using the Autogates I first had to be stamped out and back into Malaysia at the manual counter, and my fingerprints scanned. I could then use the Autogates the next time I travelled out of and back into Malaysia.
After I renewed my passport and transferred my LTSVP, I again had to be manually stamped out and back in to Malaysia before I could continue to use the Autogates.
Using the Autogates as a PR holder
After receiving my PR I checked my eligibility to use the Autogates on the Immigration website: https://imigresen-online.imi.gov.my/mdac/egate
It showed this message that I am not eligible to use the Autogates:
I had hoped that I just needed to be manually stamped out and back in to Malaysia, and that I could then be able to use the Autogates on subsequent trips.
I tried to use the Autogates on entering Malaysia at KLIA but was unsuccessful. I went to the Malaysian Passport counter and the officer advised me that Permit Masuk holders cannot use the Autogates.
Instead I showed my passport and Red IC to the officer, my passport was stamped and my IC number was written beside the entry stamp.
I also checked with Immigration online using https://eapp.imi.gov.my/tanya/create and they confirmed that Permit Masuk holders cannot use the Autogates, so whilst LTSVP holders and tourists can use the Autogates, PR holders cannot.