I don't even have a set of the halo headlights yet. I'm still doing some mock-up's with a few idea's I have for the stockers first.
There's some definate advantages & disadvantages to going either route. Neither one is perfect (in my opinion).
It would be simple to JB weld over the LED holes & then a lite coat of bondo, primer, sanding, & then paint.
It looks like we might be stuck with the bubble lense, I didn't think the actual projector stuck out that far, I thought initially it was to keep the lense away from the projector for heat reasons... it actually
As far as using the halo's for blinkers... simply wire them into the blinker wires. Easy!
I'm also looking at what projectors are easily retro'd into here as the stocl lense is average. A high quality HID package (not just PnP's) can improve these a lot. The good news is with the projector sitting so far forward in the housing 9thus why they had to bubble the lense), it should be easier to cover the back side of the housing as it shouldn't need as much "hacking" to fit the projector. It also shouldn't protrude as far out either.