First important lesson: these automated comparison sites are terrible. They emphasize things which just aren't important and make them sound like a big deal. You say:

XT 10 has a bigger pixel area which is one of the reasons I want to switch from D3200 as it has a small sensor pixel area

I see that the site lists "49% larger pixel area" as an advantage. In this case, what it's talking about is the size of the individual pixels on the sensor. All of these cameras have the same size sensor *, but the one with more megapixels has to have smaller pixels, because that's the only way to fit 24 megapixels in the same space as 16.

Some people will make a big deal about this, but it's really not all that important. Fifteen or twenty years ago, the differences may have had an impact, but these days, they really do not. For pretty much the same reasons, the differences between 16 and 24 megapixels are largely irrelevant. Unless you are very, very careful, and are taking photos under very controlled conditions, and really really care that the resulting test chart scores beat some value, it's just not something that should be in your decision criteria.

In fact, I'd go so far as to say that none of the things that site has identified are interesting (even the on-paper better video specs aren't necessarily reflected in real-world performance). Some things like the weight of the camera can be important, but the differences aren't big.

I think the main thing to consider is that the X-T100 is a current model, whereas the X-T10 is not. You say that the prices are comparable, but... are you sure you're buying new stock with full warranty?

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* Because the sensors are all the same size, field of view with the same focal length of lens will be the same. In other words, if a 35mm lens on the D3200 gives you the framing you want, you'll want a 35mm lens for the X-T10 or X-T100, whichever you pick.

The good news — or, bad news if you hate making decisions! — is that Fujifilm makes two very nice 35mm lens, a compact f/2 and a bigger and more expensive f/1.4.