While normally reluctant to disagree with you because mostly I don't, I am wondering where you found the data to support that statement? or is it
purely anecdotal?
You can call it anecdotal if it makes you feel better.
You can't just round up the IBR facts and say LOOK, see the numbers! (edit- Although I find it entertaining that the finisher percentage alone should convince every future IBR rider to pick one brand.) The current IBR is not what it was in the past. Many riders that had issues, still finished. The stats don't reflect those issues. DNF for lack of points contains a wide array of challenges riders endured that led to that. Some are not bike related, some are. Had the Vooks not had mechanical issues and the tire fiasco, who knows? Had so many other riders not suffered issues, what changes what have occurred?
My point here is that every rally is a mix of challenges to the rider. I'm suggesting strongly that you don't build in extra challenges to your plan. I just rode a 150cc scooter across the US in 10 days as part of an event. The event was very Vespa oriented. Every night the Vespa riders were repairing things, doing maintenance, later in the event swapping tires, etc. Riding a Honda I added 3 oz of oil over the entire event and checked oil and tire pressures daily. Because I did my research and chose wisely, the same set of tires did the entire event and has plenty left after 5k+. The stark contrast was painfully obvious. Did my scooters get beat up by the event? You bet! Do they currently require repairs and maintenance? Yes! Did I suffer any kind of failure during the event? No.
I've only ridden and finished one IBR. I also have ridden one MERA 10 day event where I rode more miles than my IBR and DNF'd for time barred. Both were on Yamaha bikes. In both cases I never had any issues during the event. Because of my choice to run a Japanese bike, well set up and sorted ahead of time, no added stress due to mechanical issues or the threat of mechanical issues was ever a part of my thought process during the events.
Pick any HD you want. You're not going to get that peace of mind during the IBR or other multi-day rally. The same can be said for any BMW. You're always going to be checking it, wondering if it will hold up, wondering if it will handing the heat, etc. And if you're not, you should be.
The OP is talking about starting from scratch and building a purpose built rally bike. Unless you're running in the Hopeless Class, leave the engine and trans stock, regardless of what you choose to run.
And if you want to look at numbers, look at the stock Hp made from water cooled bikes Vs cost of the bike. I know HD guys that have more money into the motor alone than the entire cost of my FJR when it was new and still don't make as much power as the stock FJR. I do not dislike HDs. They are just not an optimal choice for a rally bike. Too many things can, and sometimes do, fail. If you're starting from scratch to play this game, start with an open mind and don't just buy what you 'like'.
You can't realistically argue that belt drive is more reliable than shaft drive. (or that BMW shaft drives are "reliable" for that matter.)
You can't realistically argue that an air cooled, even with water cooled heads, engine is going to handle high heat better than a fully water cooled bike.
You can't realistically argue that picking a sub-optimal platform for multi-day rallies is going to improve your odds of finishing. Let your rallies be about the rider, not the bike.