Quite a conundrum. I understand your perspective, but you're leaving out training. You can easily manipulate body composition without touching nutrition and modifying training. Without knowing how hard you push it in the gym, it sounds like you're lifting some moderate weight with 5/3/1 at moderate intensity, without doing any cardio. If you're not doing any type of conditioning, or cardio, and doing all relatively low reps in the gym, I would imagine you're not going to lose weight unless you increase training intensity/frequency or cut calories even more. I'd rather adjust training than cut calories personally. Obviously you have to change something.
I also don't think you have a uncontrollably slow metabolism, unless there's an underlying medical issue. (Have you ever been checked for one?) Assuming there isn't, I think you need to train harder and maybe switch programs for a little while to something more intense, and educate yourself more on how to eat (all of which you can search around and find on the site). Here's a starting point:
Nutrition: (use this for food sources and possible macros) https://www.t-nation.com/diet-fat-loss/eat-to-get-big-without-getting-fat
(how to design a good cyclical diet) https://www.t-nation.com/diet-fat-loss/carb-cycling-codex
Regarding your "skinny fatness", you also wrote that you gained about 30lbs of fat, so are you being realistic with yourself about your physique? Not trying to give you a hard time, it's important to be real with yourself so you can adjust your training and nutrition accordingly.
Can you post pictures? Also, how tall are you? I've never seen "skinny fat with muscles", maybe seeing pics could help us better recommend some fixes for you.
Just my opinion is that you have a lot of work to do regarding both training and nutrition, it sounds like you think you're doing everything right and nothing is working, so there MUST be a problem, and someone out there who can give you the magic fix. You must know and understand:
-There is no magic fix, or something that someone can say, "hey do this and that and you'll be set." There are MANY things you need to try for yourself, and be consistent, and learn what's best. People that have great physiques take YEARS to build it, and educate themselves. You post on a website and expect someone to solve all of your problems in a couple of posts. Anyone that's offering advice here has all spent years of trial and error on themselves and done the research to know what works. They've also no doubt read some of the THOUSANDS of articles and forum posts on this website that can give you all of the info you need. You've already received a lot of good info from the people that have previously replied to you, but you give the impression you don't want to hear it unless it's something you agree with.
For what it's worth, my thoughts would be to think about stopping 5/3/1 for a bit and switching to something that's higher intensity. Or, add a few conditioning days. Again you didn't really talk about your training at all other than you've been training 5 years and you're doing 5/3/1. That's a HUGE variable.
If you have a caloric deficit, you lose weight/fat, it does not mean your metabolism slows down. Typically it gets faster especially if you're doing conditioning/cardio, which you should be if you're trying to lose fat. And yes when you cut sometimes you do lose some strength, there are ways to combat that with your training. If your priority is to lose fat, you need to be ok with losing a little strength to get to the level of leanness you want. Unless you're competing in a powerlifting competition, it shouldn't be a big deal.
You ultimately need to decide what your number one goal is, and realize your training AND nutrition must BOTH support that goal 100%, which they currently do not.