Most of the modes have tricks to boost their values. Egg related modes (Derelict Ship and Queen's Nest) score more if you destroy some eggs before starting them. APC values increase by completing the A-P-C targets during that mode. Combat Drop can be very lucrative if you're in a rhythm on the ramp combos during the landing phase (especially since the ramp combos also work toward Drop Ship letters for 2x Playfield). Recharge target does something beneficial in all modes.
Also remember that actually winning modes is important because that's what gives you Scene Bonus, which is based on the score you earned in every mode you won that ball, and IS impacted by Bonus X (as Zablon alludes to). 100M+ Scene Bonus feels really good.
There are a couple modes -- Find Jonesy and Bug Hunt -- that you're better off not stacking with multiball, since they punish you for "wrong" shots. Bug Hunt can be quite lucrative, but it's pretty difficult.
The movie mini-wiz modes (Self Destruct and Loader Battle) also get scoring boosts based on how many of that movie's modes you won and how many weapons you have, and since they can convert to multiballs, they can be pretty juicy -- and winning these also contributes to Scene Bonus.
TL,DR: modes may not look like they're very valuable, but they can certainly be a significant component of a big score.