Moomba gives the ability to purchase a stripped down boat to offer the customers value. If you feel you might want some of the "upgrades", I'd give strong consideration to the Mondo with some options over a stripped down Mojo. Both are going to feel significantly larger than the R20. You are right, the size feel difference is mostly in the width/beam. The Mondo has a 99" beam while the R20 as a 94" beam. 94" is small!
Rusty made some good points on the other options. The retractable ski pylon and flow would both be automatic options if I was ordering.
4k difference sounds somewhat reasonable. I would guesstimate it to be within 4k and 7k depending on the dealer.
Check out the leg room difference ....
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2016 Moomba Mojo
2006 Supra 24SSV - Traded