Thanks for your Edit!
For me, I'll just give examples. When I practice, I usually have 2 modes that I play in. The First one is a freeform, "let's go through and find places where I sound really bad" mode. I go through the music, most often at below tempo, and just go and find bad notes. This is when I often like you, realize that my intonation on certain notes are not so good. However, I don't stop. I try to loop back over the bar just before and just after, in order to put the note in context, and just replay that both "as writ" as well as "off the book" until I get the intonation right. This can include - playing with a drone (with the next open string in a double stop) to listen for intonation changes, listening specifically for ringing intonation (where the next string over has sympathetic vibrations), slowing things massively down to 1/4 or 1/8th of tempo, trying different fingerings (if you are doing positions, trying different positions), trying different finger orderings (ie if you put your fingers down in a certain order does that make your intonation better?) There are tons of other techniques I use during practice, but the idea is you are trying to hear "around" and "on" the note, listening to how your tone and intonation changes as you try different things - not just stopping and redoing the note over and over again.
The 2nd mode of practice is a performance demo. I go straight through the piece in temp, STOPPING AT NOTHING. Even if I get the notes wrong, I make a mental note and just keep going. It helps me to prepare for performances when you have to remember you are performing. If you get stuff wrong, you just keep going and make the next passage sound great. In this mode, I often use audio recording, and then go over it carefully to see where I go wrong.
In practice I alternate between the 2 modes. One is playing, figuring out how to get the best sound, the other is to practice confidence. Of course if you play something wrong you shouldn't re-enforce it, so that's why there's a lot of thinking and reflecting involved.
Other people might have different routines, but I find that for things like intonation, etc it's best to be able to play "around" the note to figure out how to get better.