Yep, just like that. No need for it on the sides or top, you'll still seal those gaps with mortar. it's just at the base where water sheeting against the glass will try to get in. The flashing need only overhang the brick a 1/4" or so for a drip edge and is usually available in lots of colors to match your brick so it shouldn't look too ugly. Our local box store chain even has a sheet you can download so you can design your own sheetmetal profile, pick a color, length, etc. and it's in your hands in a few days if you want something crazy.
All that said, with these being basement windows you're probably fine with straight mortar, but you're back to the tooling conundrum.