I do think it's common for the bass to get a quick line check and little more...but in reality most audio techs will spend considerable time dialing in the bass once the entire band start playing, so the line check is not the end of it. Bass players feel a bit burned because they think it is. To be honest, I typically tweak channel EQs for the duration of most shows in order to tailor the sound to the music.
IMHO if someone is going to run effects it is absolutely essential that all of the effects are tweaked so that the levels and tones sound right as the patches are changed. Unfortunately as I mentioned earlier this is not necessarily as easy to do as people think it is.
If you dial your effects in for the frequency response contour of a traditional bass rig, they probably won't work very well for the PA frequency response contour which is very different. Resolving this dilemma is the promise of speaker SIMs.
Also in my experience it's typically necessary to rebalance levels and tweak the EQ of effects if you change your volume significantly. So if you have your effects dialed in for your stage volume, the tone and levels may not work well for the volume used at FOH.
IMHO it's really impossible to run a bunch of effects optimally without an extended sound check and a bit of negotiation between the bass player and audio tech. But if you really learn what is going on and practice, many people can develop a intuitive sense that allows them to sound pretty darn good.
Yeah, well - that is the big problem with playing bass with a big pedalboard nowadays.
There is no real way of making sure all your effect sounds are exactly as loud as they need to be through FOH - apart from balancing that stuff on stage, for that FOH system, with the tech.
I've tried with a Headrush board where I used a limiter last in line after the cab sim to make sure all my sounds have exactly the same level. Well, that's when you learn that different EQ curves will sound more or less loud, while having the same level. And even that will change once the band is playing. A common example is the overdrive sound. When you set it to have the same perceived volume your clean sound has in your bedroom, you will perceive a drop in volume in band context when you hit the pedal - so you need to balance the OD volume with the others playing and will have a much louder setting as a result. I have a synth-style setting with a bit crusher, a fuzz, heavy compression and a sweeping filter that comes across as much louder.
All my sound presets are matched to the PA system my band usually uses and that works most of the days.
When we bring our own PA we also bring our own tech, who knows our songs and how I use my effects - which is a big help.
When we play a place with a different PA, none of this works though.