A layman on this.
I have a common sense observation.
It is NOT what the budget airlines or what the full service airlines dictate.
Maybe it is all under the control of the particular airport and what they insist must be done under that country's laws. Immigration counters are not manned by any airline staff. They are manned by the country's uniformed immigration/police personnel.
If the airport concerned wants to purposely inconvenience budget airline passengers, then it is their choice.
Now we know why KLIA is #9.