Fair enough I suppose, although I don't buy the financial argument at least as far as you went (and you said the endowment really isn't that relevant), and I also wonder if the schools that have dynasty-type programs in other sports are filled with athletes who truly would be competitive at the D1 level in the way Messiah would be in soccer. I doubt the latter.
Your last sentence is something that gets bandied about a lot, and I'm not sure why. Athletics and academics (as in admissions) have never been more competitive so I don't know if the trophies for all bit is some kind of political slip. Taking you literally, why not open up the national championships to all divisions and run them like Indiana and Kentucky high school basketball used to do with one tournament for all schools regardless of size or division?
At any rate, we can quibble back and forth about what exact word to use. The situation with soccer at Messiah certainly is unique (and I understand the mission is unique along with the other Christian-centered D3s), but I thought to comment on it right after I saw the atypical (for D3) D1-style press release on the incoming recruiting class.
I happen to be online when you responded so I'll simply say that big-time press release attempts aren't all that unique to Messiah, though they seem to be less common in soccer than in football or basketball. On the football boards here you'll see people bandying about h.s. player credentials and what they mean for incoming freshman in a way that used to only be done in D1.
As for financials, you just can't ignore the costs of running a D1 program. Most schools have extra coaches, larger recruiting budgets, they are required to have more compliance staff, tutors, bigger travel budgets and facilities. All of these are ancillary to scholarships. You need the money to come from somewhere and, as I pointed out, Messiah's endowment isn't more than mediocre for a D3 school.
Finally moving up means Messiah loses a huge recruiting tool. In D3 they are a big fish in a small pond and can talk about competing for national championships every year. In D1 they won't make that pitch as it stands now. They MIGHT get the same athletes, or those athletes might like the idea of being big fish in small ponds rather than a small or medium fish in big ponds. Once you start losing, you lose that recruiting tool and that mystique. What they have now works on so many levels, earning the school recognition a lot of faceless D1 schools never get. How familiar are you with Monmouth University in Long Branch NJ? For a few years they were ranked in men's soccer, one of the greatest U.S. women's players of all time, Christie Rampone, is a soccer alumni, and yet the school is middling in D1 most of the time. Mid-major is a kind description for most sports, and it doesn't have a lot to set it apart other than the original Annie movie was filmed on campus a few decades ago. Why would Messiah give up its recognition and recruiting edges in D3 to become more like the hundreds of Monmouth Universities scattered across the D1 landscape?
Messiah isn't all that unique among D3 dynasties. Mount Union, Kenyon, Wartburg, UWW and others all dominate a sport. Kenyon in swimming is stupidly ahead of Messiah in the dominance game, so far they make Messiah look like a flash in the pan. There are others as well but that doesn't mean they should move up.
As for your reductio ad absurdum for combining all divisions it's as ludicrous as the latin implies. The divisions play by different rules. Only MLB attempts to have a championship among teams playing with different rules (designated hitter). Setting aside MLB's stupidity, D1 and D3 are different, so they have different championships. That has nothing to do with everyone getting a trophy and everything to do with playing the same game under the same rules. And Indiana no longer has an all size tournament. Even they put that idea to bed over 15 years ago.
To sum everything up, there isn't a single good argument for Messiah to change divisions other than your comment that they are too good and put out a D1 press release. Pretty weak in the face of the actual facts of collegiate sports.