In Division II, Region 5, both MP and Martin have the same teams 1-27. The biggest discrepancies are 6 positions (1 team, 17 MP vs. 23 MRPI), 5 spots (2 teams) and 4 spots (2 teams). Essentially the top 5 seeds in each of the 5 districts will be the same, regardless of which ranking you look at it.
There may be some other districts with worse discrepancies - I don't have the inclination to look.
Shoot, in the college rankings, Pomeroy has BYU No. 9 today, the NET ranking has them at No. 5 and Massey has them No. 26. The point being, every ranking is different and thus will provide varying results.
The other thing that I would point out is that both the Martin RPI and MaxPreps strength of schedule component factors in all opponents, regardless of the outcome. It is not like the football computer ratings where you only get credit for defeated opponents' wins.
That said - and I advocated for this back in October or November - I would like to see the MaxPreps ranking have a provision for playing schools in higher divisions. Kentucky's RPI has this and it shouldn't be difficult to replicate. That's the main difference between Martin and MaxPreps, as far as I can tell.
I'm not defending or debating anyone's position; just saying in my small sample size I don't see much area for concern.