Your consideration process is very thorough!
I bought the 100-400 a little under a year ago, and like you, found that prices for new vs. used were minimally different. I snagged a used one on eBay that happened to include a hood and a UV filter, which upped the value equation enough in that direction for me. Even without an extender, the 0.41x macro ratio is decent. The extenders (I have the 2x) are suuuuper expensive, but I've been very happy with mine, no regrets about the purchase. Doubling that macro ratio such that it's getting fairly close to 1x helped convince me to buy it, I looked at it as solving two needs, both the longer reach AND the more legit macro performance. The combined price for me (Canadian dollars) was about $1600. For comparison's sake, that's roughly what the RF 100mm f/ 2.8 macro costs here (a lens I covet, to be sure). The RF 200-800 retails for $2600 (plus tax would take it north of 3 grand). Getting a a very usable macro ratio plus a 200-800mm zoom range for near enough 1/3 the money makes the value undeniable for me, even with the big caveat of more restrictive apertures.
That f/ 16 at 800mm is something to consider though, but with steady hands and good light, hasn't been an impediment for me. The ISO performance of these R-series bodies has greatly reduced my aversion to higher ISOs. With an R6 body, you also have the advantage of IBIS, lacking in my R8, so that'll be a boon as well. One other thing I like about the combo is that the densest part of the system is the extender, so the balance of the weight in my hands or on a strap is comfortable, it's not a drag to hold my lens up. It's wonderful to have 800mm of reach in a full system that weighs less than 1.5kg. Obviously an R6 body weighs a bit more than an R8, but it would only be another 200g or so.
Anyway, I feel like I've said all I can possibly say about these pieces of equipment! Good luck with your research and eventual choice.