I don't know of there is an official recommendation for a neutral zone, but .75" sounds reasonable. Or at least make sure any components on the top side are low profile, like resistors, etc. An external-facing CF slot would exceed that length, but shouldn't be tall enough to interfere with whatever's beneath.
Yes, the PLUS slots are just a hair shorter in height than PC slots, as I found out when I kludged together a bracket for my ISA-CF PLUS card. On top of which, I've also got an ISA I/O card for it's COM ports (with a wonderfully fabri-cobbled PLUS-ISA ribbon), so while everything just fits, emphasis is on the word "just." There is NO wiggle room here.
You've got a front-back clearance of 6" in either the top or the bottom slot (at least on the HX, where the BIOS/SmartWatch stack gets in the way of the bottom slot), and about 7" in the middle slot (15cm/18cm). The EX might have a bit longer on the bottom slot, but I don't have one to measure. If you were going for proper PLUS standard, you'd have at least 0.35" (0.9cm) extra clearance to either side of the external connectors, and 3 screw holes on either side with the same spacing to make room for the offset when installed on either of the headers on the Tandy DMA/RAM card. The modem card will be a good measure for your tollerances (I'm having to figure those out the hard way), since it has the relevant screw holes for installation in any slot. Obviously you wouldn't need to worry about that spacing if you're just doing a custom stack.
For examples you could try, this is a PLUS adaptation of Glitch's XT-IDE rev.4 that I'm working on (adapted from his open-source GitHub files), still a work in progress.
You can see the break-off section of PCB to be soldered in at a right-angle in lieu of a proper bracket, with exposed pads for that purpose. You'd need to be careful to make sure that this gets soldered on at precisely 90 degrees (still need to put the screw holes in there), but it should work.
I've also got an external-facing IDE header in addition to the internal one (with a cable-select jumper, should it be needed). My idea is that you could have a DOM installed internally, and plug in a CF adapter to the back for easy file transfers, etc. Or have a standard hard drive in an external enclosure if you're really nerdy and just want to hear the thing spin-up and tick. The internal header is recessed like this to allow enough clearance to have a CF adapter installed internally on that header if it's installed in the middle slot, or a DOM if in the top or bottom slot.
Another thing I'm incorporating is headers for both an active-high and active-low LEDs. The latter to be put in place of the power LED above the keyboard, (stays on normally like the Power LED, but blinks during access), so that I don't have to drill a hole in the case to mount an LED. Some people are fine with drilling a hole, but I don't like destructive mods on retro stuff. I prefer that any mods be reversible.
I've also thought of just soldering the tall headers on upside down, to take advantage of the plastic base of the header, but you'd need to be very precise to make sure the thing is perfectly square and at the correct height when you solder it, or it will misalign the card. So that's probably not a good idea.