In a window lintel situation….does the brick course that sits directly on the flashing get mortared in? If so, doesn’t it throw off the alignment of subsequent courses above due to the thickness of the flashing as well as the mortar bed?
Yes and No.
Anytime you have a window lintel you have a span that dictates the thickness of the lintel. Some small lintels (brick lintels) are only 1/8 inch thick, while others are as much as 5/8 inch thick (structural steel). Both are extremes.
When you have a thick lintel you usually lip your brick. Most people do it on the top, but I do it on the bottom so a drip edge will fit better (by adding two bends to the drip edge it conforms well to the angle). In some cases bond works out without a bed joint, while others have a bed joint. Regardless, the head joints are always filled.
It is also not unusual for the architect to spec caulking the lintel bed joint, but I do not recommend it for new construction or restoration work because it can block the weeps and the breathability of the mortar that contacts the sealant.