I did this route (from KUL) on a similar fare just before covid in March 2020. Im not sure if it has changed, but at the time all passengers transiting in MNL with onward connections to either Australia or the US (and possibly the UK) need to go through a secondary screening at MNL. This was in T2. This involved all transit passengers being squeezed into a small room to identify their own check in luggage for it then to be opened and then manually checked by ground/security staff. Chaos would be an understatement, and those who had their luggage shrink/security wrapped were not happy when it had to unsealed to complete this check. They were then offered tape to manually reseal it. If you dont have a tight connection, you could be better off short checking your luggage to MNL then going through immigration and then checking in in departues (this can get very busy though).

Having spent alot of time in PH, these things are often completed much faster if you keep your cool and are friendly/respectfull to the staff. It became clear that those that were getting irate were not attended to quickly, and of course there was no real queing system in place. Also have printed paper copies of e-visa's, return tickets etc as you will be asked to show them at the gate regardless of whether or not they were verified at check in.

A350 Flat bed and service was excellent though.