Hope I can answer some of your questions.
1. Mutli reflector setups will out throw and out flood a single reflector of the same size. e.g.
For arguments sake, take a Convoy S2 with a 20mm wide reflector. If you now got 3 of the Convoys and taped them together to make a "triple". It would have 3x lumens, a bigger hot spot, brighter spill and greater beam distance.
The beam profile however would not be what most people would consider a "thrower". As in this case you have only increased beam distance with pure lumens. The larger hot spot is due to having multiple emitters.
2. If you took one of the Convoys and pulled the LED and electrics out and fitted them in a host with a 4" wide reflector (no other changes). The beam would have a much smaller tighter and more intense hot spot, duller spill, but it would throw much further. And it would have a completely different beam profile. Although the lumen level would still be that of 1xConvoy.
3. If you want to run multi emitters, each emitter needs it's own optic or reflector. You can't just have a large single reflector with a single hole in the bottom. You'd never get them to focus and likely end up with an ugly beam. It's maybe not completely impossible, but something very advanced and you almost never see anything like it.
There are some LED's that are made up of multiple dye sections, the older MC-E and the current MK-R. But focusing them can still be an issue and they seem far more suited to flooders, not throwers.
4. In terms of output. If for example you had a driver that could put out 3 amps.
3 amps in one led will normally be high output and a fair amount of heat.
If you converted to a triple, you could wire them in so that each emitter gets 1 amp each. The driver would not be working any harder and still putting out 3 amps total.
In theory, most emitters are more efficient at lower current levels. So 3 emitters @ 1 amp each is likely to produce more lumens, less heat and better runtime than 1 emitter @ 3 amp. But the reality is, this isn't going to be a huge difference.
The trade off is, if you want to keep the same physical sized flashlight, the optics/reflectors for a 3 emitter setup are likely to be smaller. Thus a more floody light, despite the fact it might have a small lumen advantage.
Now depending on your exact setup, you might be able to wire the leds in so that they each get 3 amps. This would require a driver (and battery) offering up 9 amps in total. Three times as much as with one led. This will offer much shorter runtimes, lots more heat, but also lots more lumens (up to 3 times as many). However you still have to contend with the physical size of the flashlight. Smallish reflectors/optics, even with 3 heavily driven leds is still likely to produce a floody style beam, even if it lights stuff up quite far out.
If throw is your key, then smaller LEDs in relation to the reflector will throw better. E.g. an XP-G2 will out throw an XM-L2 in the same size reflector, all else being equal.
And de-doming is a contender too. You can de-dome a Nichia I believe, but not sure how easy it is too do, or how well it will perform.
De-doming will cause a tint shift.
What you might want to do is see if you can buy something that physically is right for what you want. Then look at swapping the LEDs and maybe driver.
Nichia's are quite nice, but honestly I think the XP-G2 R5 5A2 looks just as good tint wise and will offer up more lumens and more throw.