Acoustic basses often get used in situations where there is just too much stage volume, and players expect the same "on stage" level they can get with a solid bass. It is better to have most of the sound in the main PA and just enough stage level to hear - but that just feels uncomfortable if you haven't done it a lot. Also, the on board preamp allows a lot of tweaking, which usually just exaggerates rather than enhances the sound.
Its always going to be a tricky situation, and you did well to supervise without any conflict. I did a complicated show a few weeks ago, many bands..most with electro acoustic guitars and small AER type amps (big venue). The engineer had to deal with all of them setting a sound on the amp (too bright, too bassy..to make a small amp sound big) then watch them tweak the on-board preamp to be even brighter as he tried to tame the sound for the PA. Makes you appreciate why many engineers insist on using the "pre" and not "post" DI on bass amps.