Welcome! You're certainly doing a lot of good things by going with less shoe. The more sensory info your feet have from the ground the better your running will be. As Gordon said it's no accident that the pain goes away when you're totally bare.
Here's something I wrote up going into more detail about why no shoes are better than any shoes:
https://www.thebarefootrunners.org/entries/the-best-shoes-to-transition-no-shoes.1299/
Even those super-thin Xero sandals have way more grip than bare skin. They blind you to damaging, inefficient horizontal braking forces which are the real enemy to running. For decades shoe companies have been operating on a completely flawed assumption that vertical impact is the source of injury. More recent research has found that it's horizontal forces not vertical that are a more likely cause:
https://www.theglobeandmail.com/lif...ticle-how-running-gait-increases-injury-risk/
Think of it this way: when you run how much vertical oscillation can you measure with you head bobbing up-and-down? A few inches? How long is your stride length? A couple feet? Right there you see that there's an order of magnitude more horizontal movement going on than vertical when you run. Adding padding and cushioning is a solution looking to fix a non-problem. I fully believe it's that super-grippy tread and a snug fit that's responsible for more pain than anything.
As for top-of-the-foot pain I had that at the start, too, along with pulled calves and achilles tendon pain. That was very likely due to a common misconception and over-correction almost all of us have fallen for:
https://www.thebarefootrunners.org/entries/stop-worrying-about-the-heel-strike.1273/
When you get rid of the padding it's understandible to think "I need to compensate." So you tend to be up on your toes/forefoot more. All that's going to do is stress out your feet and lower legs. Your whole body handles vertical load great and it does that best if you don't try to micro-manage that. Your calves should be used to bounce you forward not stressed-out by over-using them as extra shock absorbtion you simply don't need.
For me I think the top-of-the-foot pain was just from stretching my feet out to land forefoot while still over-striding. It was an awkward position and my feet were taking a pounding slamming on the brakes in front of me like that.
If you take the sandals off you don't want to do that because you chew up the skin underfoot. Now, over a long period of time skin will get thicker and become more puncture-resistant. It will never become magically immune to blisters. Evolution crafted our feet and legs to work together with the specific properties of bare skin. That means your legs are strongest when your feet are firmly on the ground under your center-of-mass not way out in no-mans-land in front or behind you.
Shoes with super-grippy tread train you to over-extend your legs. Your body is cued into trying to grab at the ground with that artificial grip in ways that just don't do your legs justice. A lot of grip like that is useful if you're competing and you want to put as much power into your steps as possible. But for training if you're 100% shoes you're just teaching yourself to run worse. Cushion and structure complicates that but the real danger is in the tread itself.
So think about how people like me have done several full marathons in bare feet and I didn't get any blisters. My feet aren't super tough. If I step on a small, sharp rock it hurts! How I did it is in learning to work with exactly how tender and sensitive human feet are. Work to baby those feet and handle the grund gently with finesse not force. The result is not just that the whole rest of your body will avoid damage but you'll be more efficient, faster and stronger as a runner.