You're thinking about interesting things!
The chain is a bit off in your description of the process. I'll start there.
The musician is miked and recorded. The mics are stone flat and capture an accurate, clean recording of the music. This is called "tracking".
The various tracks are mixed in the mixing board, not just for relative volume, but for tonal quality too. The engineer creatively EQs the various tracks to make them "read" as separate parts, not blend all together as a mush. This might require straying from accuracy, but it is a creative decision made by the musicians, producer and engineer.
The mix is monitored on speakers calibrated to a flat response. This calibration is necessary so the whole thing doesn't sound different if they have to go to another studio to complete a mix. Hopefully, what is heard in the studio is going to be heard at home.
The final mix is adjusted to make sure one song isn't louder than another on the album, or so that one song doesn't sound sharp and another muffled. This is called "mastering". The goal is to get all the individual songs to sound like one unified album. Again, this is monitored on calibrated studio monitors.
Next it is burned onto a CD. That is an exact copy of what the engineers intend it to sound like.
The CD is played back on a home stereo. Ideally, that home system is calibrated, just like the studio monitors. If so, everything sounds exactly the same as the musicians, producer and engineer heard. All of the accurate sound is accurate and the creative decisions made in the mix are all presented accurately.
Does that make sense? In particular, the mastering part?
OK, now to the seocnd part of your question...
When you buy a set of speakers, they are not flat. It is very difficult to manufacture full range speakers that are totally balanced. Even if they were, the room itself would alter the sound and make the response unbalanced.
When you build a listening room, the first thing you do is look at room acoustics. You try to cancel out the reflections that mess up resonse... Absorbtive panels, bass traps, etc. These are the broad strokes things that correctt for the big things.
Now if you are married, or if you want a listening room to look like a normal living room, treatments can only go so far. Even if you are willing to run acoustic panelling everywhere, it can only get you close... not perfect.
So you make up the difference with equalization. EQ is a lot easier than knocking out walls, panelling over big windows or flying acoustic panels from the ceilings. It also is MUCH more flexible and precise. You do what you can with the room, then you EQ the rest of the way.
The easiest way to control EQ is to add it as the absolute last step in the chain... right before the speakers. If you correct for EQ by using a colored CD player, when you use a different source, the correction doesn't apply. That means that your CD player would sound totally different than your FM radio tuner, DAP or turntable. You want a completely neutral system, so when you apply EQ at the very end, the EQ is being applied to everything you play on your system.
Now, let's say that you prefer a little bit of coloration overall in one place or another in the curve. The odds of finding equipment colored to your particular taste is like trying to find a needle in a haystack. Some people like a 5dB bass boost at 100Hz, other people would prefer a larger boost in the sub bass- say a 15dB boost at 40Hz. Still other people prefer "in your face" mids, U shaped curves with lots of bass and treble, or "detailed" or "warm" treble. It's just not possible to have DAPs, CD players, DACs or radio tuners all adjusted to a different taste in sound signature. That would be chaos.
So they make everything neutral, and you apply an overall correction using an equalizer to make all of your equipment sound colored precisely the way you want them. EQ curves don't have to be flat. They can be any flavor of the rainbow you'd like, and you have complete control over how much of a coloration or how little you want.
Once you've set an EQ curve... whether calibrated to flat or colored to your taste... you leave it be. You don't monkey with it. If you want to adjust for specific recordings, you use your tone controls.
In theory, a carefully chosen EQ curve will give you exactly what you want. That is great if engineers are infalible and all recordings are created to spec. But engineers are human too. So you have tone controls to quickly adjust the tone without monkeying with the carefully balanced EQ curve you've set up with your equalizer. With good recordings, you can bypass the tone controls. But with less than perfect ones, it's nice to be able to do a quick fix. Neither tone controls nor EQ degrade the sound. They just allow you to change the response.
EQ is for a fixed overall correction. Tone controls allow you to do quick and dirty corrections on the fly.
Does this help?