This is 100% true. Also consider that this is a variant specific issue. If there's a commit in a shared repo (i.e. the Telephony repo) that is if reverted fixes the issue for us then they would also need to make sure it didn't cause issues for the other variants.
Some additional information.
I assumed you needed to boot into 3.x first for the fix to work. Data about your system apps is also stored in your /data partition and created on the first boot. When you dirty flash this data persists. My thought is that some data from com.android.phone or com.android.telephony persisting is how the fix works.
DavidFlory has reported the bug to Temasek with relevant logs. LillieBennett doesn't have her SIM card in her Note 3. I don't have this issue on my phone. Like I said before this issue is really something that CM should be working on, not Temasek. There is no CM12 support for us though.
3.5 and under were bugged to crap (GPS issues, video stream issues, com.android.phone FCs). This is why Temasek stopped building. This is why CM has no official support. We are using Sprint blobs currently (this was the major change between 3.5 and 5.9) but I suspect there's some kind of incompatibility that won't be resolved until we get Verizon blobs.
I would maybe try getting in touch with the CM maintainers (the Temasek thread mentions most of them; Tony Laher (slayher) is the main one). At the very least, they could probably provide some good insight into why they don't offer CM12 for us and if/when they will. I would grab logs of a clean flash of current Temasek, clean flash of 3.5 Temasek and dirty flash of current Temasek on top of 3.5. You could also grab a log of cmRemiX. Let them know that current Temasek builds use the Sprint NH4 blobs and Temasek 3.5 and cmRemiX uses the Verizon NC4 blobs. Use adb to grab logs if you are getting reboots. Use logcat -v long (this makes them look a bit nicer). You could also try deleting that newril line from build.prop like I mentioned a couple pages ago and report back.
As far as giving up goes, I think it's kind of unfair to say that; sometimes you might not realize what's going on. Red_Out and DavidFlory nailed down a workaround for the SIM issue. radionerd gave me a workaround for 5GHz WiFi. I put in quite a bit of work (all easy stuff for a real dev but it was hard for me) that resulted in Temasek building again and I spend more time than I should staring at the relevant repos and looking through logcats. And that's only off the top of my head of things I am aware of. Case in point, I didn't realize all you did getting TWRP up for 4.4 (thanks by the way). It's not a large community but I like the people here. It's frustrating for everyone but especially since there are so few of us it's important to get along.
P.S. I was looking at CM's vendor repo. They are still using NC4 blobs. I think jumping to using Sprint blobs before trying NK1 may have been jumping the gun somewhat. If I have time this weekend I'll do a test build with NK1 blobs. No guarantees though, real life and whatnot.
@other people
Personally, I think if you have your device working you shouldn't risk a clean flash.
Awesome! Alliance is a sweet ROM. Those guys did great work. When I first ran it I thought "Wow. This is the first TW rom I've tried that seems like more than just stock with a system app or two removed." leankernel is a sweet kernel. I've liked imoseyon since 2011 when I used to read his blog. I'm currently running this setup as well.