CAREFUL!
you can physically plug the atx power supply's connector into your mac's mobo, but
you will short the +5V to ground through the motherboard!
----disclaimer----
i upgraded my agp g4 to an atx power supply some time ago. forgive me if i have confused some of the details, it's been a while and i can't open my g4's case right now. as yahoo maps says, reality check to make sure roads still exist
----/disclaimer----
while the older G4s (pre-ADC) use a power supply that looks almost the same as an ATX power supply, and uses a 20-pin mobo connector that looks the same as the ATX mobo connector, they in fact are not quite the same: they differ by two pins. so you can physically plug the atx connector into your mac's mobo, but
you will short the +5V to ground through the motherboard. [in other words, apple are either idiots or evil].
but it's only 2 wires, so easy to fix.
there's an article over at xlr8yourmac with the info for modding an atx power supply to not fry your mac. (it's called something about putting a mac into an atx case). it's a simple soldering job, and the instructions are quite clear and easy to follow; I recommend doing the modification on an extension cable. you can get them for a few bucks from a store like abccables.com. to me it was worth the few bucks to save a lot of worries and the warrantee on the power supply; also it's easier to solder).
installing the atx power supply in the el capitan case is the same as the apple power supply except for 2 things. there is a little doodad that screws onto the side of the tray the power supply sits on to hold it in place that uses a screw hole on the apple supply that the atx doesn't have. so the atx supply will be a bit loose, but it's not really a problem. [you can see this in the apple docs on replacing the power supply-- dig them up in apple's site].
the other thing is that the atx supply i got (an antec) didn't have a connector for the enormous single case fan. i improvised by destroying the plastic if one of the fan connectors until i could get the proper pins to line up, and then just wrapped it up in electrical tape. "ugly," works fine
so, a bit of work, but you can save a lot relative to the price of apple's power supplies. you also can get a power supply more capable than apple's. 200 watts is not enough for a processor upgrade, a radeon 8500, 4 hard disks, and two bus-powered firewire drives

. lol it wasn't fun when starting an opengl screen saver or burning a cd would cause my firewire devices to disappear 'cause the controller chip was underpowered. now i've got 480W of joy. never mind the ugly fan installations needed to cool this thing down

.