There is kind of this running joke, at least in heavy metal that guitarists over scoop their tones all the time. I was wondering why this thing that is apparently universally bad is also so prominent. I make an effort to avoid scooping my tone because I know it's fundamentally bad, but I don't really understand why-it doesn't sound terrible to me. Is it as bad as it's made out to be? What's going on here?
As usual, it's not black or white.
There's nothing wrong with a mid-scoop sound... it depends on the context. It's not that your tone would be bad, it's that it can be bad *in the mix*.
When you play your bass alone, mid-scoop can actually sound really good. It's only 'bad' if it's a sound that does not work in a specific mix. Most times, you need a healthy dose of mids, low mids in particular, so that the bass has presence and punch... but it depends on what other instruments are there and how they're EQ'd. If you had other instruments very prominent on those frequencies, the mix may not sound very good if you pile up your bass on the same frequency region.
Imagine, I don't know... a trio, to make it simple... drums, a clean guitar, and bass. You can easily EQ that mix so that each instrument occupies certain territories without interfering. You can probably reduce your mids there and find a way to make the mix sound great. IN a busy metal track with two guitars... it can be harder, especially if the guitars choose to have a lot of bottom end, essentially encroaching on teh bass' territory. Without a healthy midrange, your bass will have no definition at all and all you'll hear is the very bottom end and some metallic clank on top. Sometimes that's exactly what you want, so it's good. Other times that's not what you want, so it's bad, and something has to change. Pitch definition is carried mostly on the mids, so it really depends whether you need the bass to be a bit clearer, more prominent, or providing a warm woolly blanket upon which the guitars and vocals will do their thing.
There's not right or wrong, just right or wrong *for a specific purpose*.
It's not just bass, it's the same with guitars. The typical newbie metal guitarist (I was one!

) typically finds a sound they like at home, and it typically is very heavy on the lows... because playing alone it sounds better that way. Add a lot of distortion, yeah, sounds great! Turn down the mids a bit... yeah, chunky riffs just fly off the fretboard. Awesome.
Then... join a few other guys, another guitar, drums, bass... you've got this awesome tone, turn it up and... you can't hear a thing, because you all did the same thing. Despair. Why? Where is my awesome tone???

Leaving aside the fact that we perceive different frequencies better at different volumes, so you can't just find your sound in the bedroom and simply turn up (that would be another thread in itself), you need to 'carve' a niche in the mix for each instrument. That's what sound engineers work very hard to achieve night after night, band after band. It's not a difficult idea, but it takes a lot of practice to be good at it (that's why good sound engineers are in demand always and can earn a lot of money), so don't be discouraged if you need to work hard at it. Like most things, it comes with practice. Try to understand what frequency ranges are important for different things: what gives you clarity in vocals, what gives you a punchy prominent bass, how to separate the very low end between the bass guitar and the bass drum, etc. Then, you can choose whether to scoop teh mids or not, on purpose, with a goal in mind.
I found very interesting to listen to multitracks of well known songs that you can find online. The mix sounds good, then listen to each instrument alone... very often the guitars don't sound all that nice, and the bass? the bass often sounds dirty and middy... but put it together and... magic... it fits.
In short: it's all about the mix. A mid-scooped bass can be the perfect bass sound for one song, but not for another. Trust your ears and not hard fast rules about settings on an amp, or a pedal, or anything. Think about how the instruments fit together.