This is what I read on CRG about the topic---

Differences in V8 Engine Mounts and Frame Mount Brackets

All '67-'68 small-block (SB) and '69 307ci and 327ci engines used the same frame mount bracket (approximately 2-1/2 inches wide) attached to the subframe. The 1969 302ci and 350ci engines used a shorter (~3/8 inch) and narrower (~1/4 inch) bracket. 1967-68 engine mounts will assemble to the 1969 302/350 engine mount bracket, but this is an incorrect assembly that results in driveline vibration and clutch chatter because the engine sits too low and can move on the bracket.

My question(s) is why did they lower the frame mount stands on the 69-302 and 350? Does this actually lower the engine? What does this do to drive line angle, since the transmission crossmember isn't lowered along with the frame stands?

In 1969 they changed the engine mounts to an interlocking type. This combination (engine mount and frame mount) made up for the lower mount. The thickness of the mounts changed by almost 1/2".

So the engine doesn't actually sit any lower than a 67 or 68?

No