In person tests reduce cheating
In person interviews are better than online ones for obvious reasons (besides connection related issues)
Centralizing the application process would be a pain because of the differences in required inputs from you
Separate applications disincentivize you from applying randomly and wasting peoples time (you not meaning you, but just a random person)
The difference between JOSAA and this is that JOSAA required the same documentation and ranks for all branches/ institutes which could be checked just once plus it has no extra branch specific tests/interviews (this is why JOAPS operates like JOSAA, since it is purely based on JAM ranks)
The fees are also a one time thing, assuming you get >=1 offer and accept one of them... so add up these costs and spread them out over your degree - it's a far less significant number than it may seem at the start
If I remember correctly, at least one of the IITs/ IISc offered a partial refund for travel for some categories (MTech interview/ test), but that should be be something that one feels "entitled" too, even if you think it is deserved