Even in a system that's been architected with specific channel layouts, there's almost always some weirdness somewhere, and some differences, and some number of radios always seems to arrive mis-programmed and needs a trip back to the radio shop, and this if the folks receiving the batch of radios are paying attention and can afford the reprogramming. Not all do, or can, either.
Not all radio shops pay attention to what they're doing here, and even the good shops can be using radio service software most charitably described as atrocious.
And yes, anyone that thinks you can have everybody on one of the mutual aid frequencies is headed for trouble. The pile-ups are always massive. Add in encryption and tone squelch (CTCSS, PL) and you might be stomping on the other agencies without knowing it.
In a typical organization, you'd want your dispatcher(s) or communications officer(s) or (if not delegated) one of the senior officers on the shared channels.
Modern radios can be surprisingly complex tools, and the FCC migration to trunked radios and digital trunked radios, and adding inter-operations features (gazillions of channels, etc) and digital communications and deadspots, and the over-the-air rekeying and reprogramming, emergency button(s), and the seemingly obligatory remote kill can all combine to makes your average high-end radios hairy.
Certainly various radio users don't regularly train with and aren't familiar with the "odd-ball" channels; the "national" and mutual aide frequencies can have different names, or weird local oddities, and many of the end-user folks are often trained to stay off the other channels.
Training is certainly part of this, and of using the radios correctly. Conversely, you're probably not expecting the folks to be picking random channels. In the newer radio systems, you can be told (by dispatch or by your supervisor) which channel to use, or dispatch can reprogram your radio and your talk group(s) on the fly.
And as for training, every emergency services department I'm familiar with has been chafing under the political and technical and documentation requirements arriving from outside entities; blanket mandates requiring time and thought and budget for stuff that's probably never going to happen to a given individual or agency, but the obligatory training and documentation requirements pull the folks away from the stuff that they can and will be dealing with. Like dealing with their radios. And delivering whatever service the folks hired on to provide.
Yes, modern radios can be far more complex than it should be. So is the rest of the mess.
Startup ideas here? Sure. The two-way radio version of a ruggedized iPhone; a radio with a "modern" UI.