Can I use store bought ghee instead of clarifying the butter myself?

Hi. I'd recommend clarifying the butter yourself. Though they may be similar, they're not the same. There can be a variation in taste.

I definitely would not plan on using store-bought ghee for something like this without testing it on a scaled down sample of this. Every ghee I've ever bought (and I buy from Indian groceries that have a high turnover of inventory) has had a flavor that seems quite different from the conventional clarified butter one makes at home. It's fine for cooking, but I'm pretty sure I wouldn't like the taste in baklava. ;o)

Yes, though there may be slight taste nuances. Although they are close to the same thing, they are ever so slightly different. Clarified butter is heated only to separate the solids and liquids, with the process stopped before the solids brown, that is caramelize. With ghee, the process is taken to that point. So you might get a few caramel flavors in your ghee you would not note in clarified butter. But for baklava, that would not be a bad thing, if anyone even noticed. So yeah, use the ghee. I would.