hey, sorry - haven't had a lot of SM or forum time this year, so I've missed some tags around here.
Yep, there is not a lot of overhead clearance on this platform compared to other Toyota models—it sort of tells you what the company's use projections were, considering they expect these to carry some load more or less daily. Position-wise, it's a fine line between kissing the cross-member without extending bump stops and missing the coil if the mount were angled to slide past the cross-member. (I like that you've retained the inner coil bumps, btw - I retain those as well as they don't really interfere with articulation but improve bottoming on square hits.)
Design-wise, I have to deal with some compromise here to get a height-adjustable (and therefore tunable for different loads/setups) part, so this variant is shaved down as much as I feel comfortable with while retaining both mounting heights. In this scenario, you could trim the rearward ear to clear, but I'd probably leave it as-is now that it has found and defined its operating space unless it bothers you, so as to retain the upper hole option if you ever change it up suspension-wise. From what I can tell, it doesn't look like the in-use contouring you've done there has limited the movement of the joint.
The installation looks good.
Are /were you getting any noise on contact that you're aware of?