OK, I have an update on my issue, but couldn't decide if it was worth posting.
Basically my issue is now a non-issue, but I don't know why. Essentially I was changing up some various cabling for a number of things, and in the process decided that I really wanted to get the switch out of the middle, but mostly cause I'm bunny about wanting to see all blue lights vs one orange. (Orange = 10/100 vs Blue = Gigabit)
So anyway.
I removed the switch. Shut down (unplugged) the modem and the A+ for 10-20 minutes each. Plugged in the modem, and gave it plenty of time (maybe 15 minutes) to boot and establish connection. Then plugged in the A+ and gave it some time (maybe 10 minutes) to boot. For whatever reason, it connected and negotiated just fine.
I was on R069 when I did all this, and have since upgraded to R069cb and all is still working well.
I honestly, don't know why it didn't work when I tried all this the first time, and I don't understand why it's working now, but it is, and I'm happy. Comcast has their modem back, and my SB6141 is working without issue. I'm still using all the same cables as before, so I know that's not an issue either. Who knows.
All blue lights now.
Long story short is that the A+ can work with the SB6141 without going through a switch.