EMC2's EStop can be configured numerous different ways, high or low for any signal and not all signals need to exist even. You can certainly configure it to do what you just suggested.
That said I'd comment that whether the default setup you seem to refer to (there are defaults that appear in Stepconf but you can change them to whatever you need, I believe that some of the manufacturers and hobbyists have just followed a basic standard at some point in the past so that arrangement has just been applied as the defacto standard - I made my own Opto-Isolated BOB so I put things in what seemed like a logical order for me and easiest to etch on a single sided through hole PC board wihout needing a lot of jumpers to route signals while still keeping a ground isolation strip between traces) in the config is low or high, you take into consideration shorts and broken wires - what you just described has the estop switch sending a HIGH signal to the machine so a broken wire, dead power source, short or other malfunction could result in no Estop signal being present. Safe practice dictates that you set it up to be a LOW signal seen at the controller is the Estop condition. What needs to go in and what EMC puts out are configurable either way. Looking for a low signal would protect against a dead power source, broken wire, popped fuse, short, etc. IIRC my Gecko drives (203v) required a low signal to be active which I didn't like, my thought is that they shouldn't go live until they have their supply power and a positive voltage signal from me (the control computer) to go live and start resolving position pulses.
Many people (from the EMC mailing list atleast - myself not included though - at least not on a benchtop mill - a knee mill like a Bridgeport and I'd probably agree with them) prefer to shut EVERYTHING down on an Estop except the computer, and use the Estop switch to run a charge pump (looks for a constant X frequency signal present as a watchdog) and if that shuts down (which if the computer goes haywire or the estop were pressed would happen) then the power supplies and drivers and spindles and everything are shut down.
I use the charge pump to disable the power source to the drivers and spindle but not on Estop, only when EMC is shutdown or lost (ie - if estop doesn't stop the problem for some reason then I have to hit the PC reset or power button) and Estop just disables EMC from sending any signals. If the computer gets lost (which it did once while loading a really complex .ngc file since my PC is an old curbside find - it's never gotten lost running a program, that one it got lost on was a complex engraving that had multiple loops to take something like 100 passes in a loop for each path using the O word commands EMC has available - it was the Detroit Redwings logo so if you're familiar with the Winged Wheel you know there is a lot of fine detail to that resulting in detailed program and the loops were too numerous for the machine and it timed out trying to figure it out, I tried it on my test machine - my office desktop setup dualboot in EMC and it loaded quickly without issue - P3 650mhz w/ 380mb vs a P4 2.8 w/ 3GB) the charge pump signal stops and all the drives shut down. This also allows me to have the computer on and work on other things without the mill being powered up, so long as EMC is off, and I can't power up the mill without the PC which prevents extraneous signals from doing anything unexpected. So basically I have one power switch (the computer) and then EMC is the virtual power switch for the mill.
Just my cautious suggestions - being safe now is easier than getting patched up later. YMMV.
Greg
(edited [repeatedly] for some clarity - I tried to touch on so many different points and this got LONG - I just recently took my meds so my brain isn't fully with it - sorry - hope you understand where I am trying to steer you )
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