Yes, that's exactly right. I also use eyelets a lot for vias, which stick up about 1.5mm off the board when it's clamped to the bed, so it would be nice to know that those will be in the clear as well.
I did the technique you described, but for different reasons. I didn't trust that the unit wouldn't still slam into the chip, and I couldn't afford that risk. I'm down to my last nozzle, and breaking it this weekend was not an option. So I waited until the end to place everything.
I pasted the 0.5mm pads first to ensure they were cleanly laid down, then did the rest of the board in sections (about 100 parts).
Which brings me to another problem: on large numbers of pads, I found that the paste output would progressively weaken. I would often have go back a few steps (to force the V1 to re-home the nozzle) and re-prime the syringe, making sure to dump out a fair amount of paste. I'd then be back to having to recalibrate the output a few times before continuing.
This is much more of a problem when you have to wipe it down with other pads nearby that already have paste, since getting paste up is not as easy as ink. Sometimes if I was lucky I could squeak by with increasing the flow rate in the GUI, especially once I was on to the larger pads.
Though I know I'm pushing the limits with 0.5mm pads, I found that calibration was particularly tricky there. With larger pads the nozzle can afford to mess up a swipe or two. Not so with the small pads, as there's only one swipe. And that's where you really feel the pain of the diminishing output. For the 208 TQFP I ended up doing one side at a time, cursing when I'd have to thoroughly wipe then start the row again just because the last 10-15 pads were too thin to be reliably reflowed.
Keep in mind this was a new nozzle (I discovered the hard way that if it's even a little bent, it's toast), and I thoroughly flushed paste through it. So I don't know what what up with that. I did manage to successfully lay down all the pads with some patience.
(and it would be really, really nice to have the option to paste the top of the vias, though I know I'm probably in the minority there)
Thanks again for you and your team's responsiveness.