The matter beamer should stop transmitting matter once the spawner is full of that matter, or make it possible to detect how much of a certain matter in the spawner. To make automation possible without spawning a ludacris amount of mobs at once.

This is part of the challenge. Note also that RFTools Control has ways to accurately automate this (it can see how much matter there is). But even without that you can still do the calculations and make sure to transfer the right amounts

it`s already the spawner that requires the most setup to use, why make the automation extra difficult? most other spawners only need RF, just to use the RFTools spawner you need a farm for living matter, a way to collect bulk matter(can be done thru a builder but requires a lot of power) and key matter you get from the mob you spawn, why make it require an add-on mod to automate it? It should be in the base mod. That's the way I see it anyway.

You can do it in the base mod already by keeping track of what you inserted. Additionally if you have a mass production of living matter (which is easy to get) you can just feed it in without worrying of feeding in too much