Nutrition and Calorie goals priority

I think it depends on what your end game is. Say you are trying to lose weight... so you focus on calorie goals. At least until you reach your goal and then you switch to nutrition goals.

When you are down in a healthy range then you mainly target nutrition goals (or when trying to specifically build muscle)

Currently i'm working on the weightloss aspect of my journey so i prioritize calorie goals over nutrition goals. Although that doesn't mean i don't try to keep my nutrition in mind. I'd rather hit close to my nutrition goals then be completely under or over them.

I don't really separate nutrition and calorie goals in that I prioritize both. However, my nutrition goals are ones I set and aren't determined by MFP's numbers. For example, important nutrition goals of mine include getting lots of varied vegetables and a decent amount of fruit and keeping my protein numbers to a particular level, and the first two are never in conflict with my calorie goal and the latter is more of a overall goal than a particular day goal, so it really isn't either.

To demonstrate how this works in practice, I set my own macros because I think having enough protein helps me not lose lean muscle mass and also helps me make sure my diet as a whole is one that's sustainable and doesn't tend to make me feel hungry on the calories I'm eating. But I see nothing particularly problematic from a nutritional POV if I happen to be higher on carbs or lower on protein on a particular day, so unless I think I need more food for some other reason, I wouldn't go over my calories just to eat more protein on one day. Instead, if I see that I'm not doing a good job of hitting my macros on multiple days, I'll look at my typical day and figure out why that is and adjust.

Similarly, when I exercise more I tend to want more carbs and the percentage breakdown of how I use exercise calories is not identical to how I use my initial goal calories. Since my reason for setting my macros as I did was to make sure I got a certain amount of protein and fat, it is not inconsistent with my nutrition goals to eat over my 30% carbs when I have lots of extra calories, and I don't fret about it.

Similar things with sugar and fiber. My nutrition goal isn't to hit a particular number or less of sugar grams, it is to make sure I'm not eating a disproportionate amount of non-nutrient dense foods. Looking at sugar and where it's coming from can be one way of monitoring this (although I don't find it particularly difficult to spot anyway), but the specific number is less of a concern to me (I never seem to go over, though). I just started monitoring fiber, and will play with it some, but so long as I'm eating lots of fruits and vegetables I'm not yet convinced that the specific fiber number is such a concern. It will depend on how I feel at different levels. I personally ignore saturated fat and usually don't log added salt (which I use in cooking), although it's worth seeing if you are eating lots of sodium from other sources IMO.

I also have my own little things, which probably everyone develops. I like to get meat from a local farm and as a result I often get fattier cuts than I might buy from the store with unlimited choice. For me this does create a little bit of a conflict with calorie goals, but it's workable for me and so a tradeoff I'll make. I think yolks are healthy so don't cut calories by tossing them (although sometimes I'll add egg whites for more protein/bulk), stuff like that.