EnderIO redstone conduits had issues in the past, so some players might not trust them - and more importantly, they just don't have easy ways to implement some things. Even basic gates and wires from ProjectRed are an improvement, and Integrated Circuits allow cramming a big arbitrary redstone logic setup into a single block.

Strongly agree with this. In addition to the buggy behavior the OP mentioned, control/automation setups are still far too bulky even with the reduced footprints that are offered by EnderIO redstone conduits with gates.

Agreed. Redstone conduits are still incredibly buggy, so much so that I seriously considered switching my snad farm to vanilla redstone.(Some of the snad just didn't receive redstone pulses and I had to reset all the conduits)
I will make a PR soon
Edit: no I will not, too much work for adding basically a more reliable but much more complicated version of redstone conduits

Something interesting I've found when dealing with redstone conduits is that they seem to work reliably under certain conditions. This is what I had to do (or not do):

1. Set up all the conduits, inputs, outputs, and any redstone filters before doing anything else.
2. Make absolutely certain that none of the conduits cross chunk boundaries. If crossing chunk boundaries is necessary, use a repeater at the chunk boundary to connect the conduits in the first chunk to those of the second.
3. Do not use redstone dust at inputs or outputs-- very buggy. Instead, use repeaters, comparators, levers, redstone torches, etc.-- basically anything but redstone dust. Redstone dust can still be used elsewhere; it just can't be connected directly to conduits.

I'm not certain that this works for everyone, but it did for me.