Homelink unable to recognize remote on step #1 - Orange Flashing
PSA: This likely applies to all cars with homelink, but posted here because it's was on our Brz.
If you get stuck on the first step of homelink setup where you are waiting for the orange light to go to green when pressing your remote button: it is likely you have a third party (aka cheap) or damaged remote than cannot produce a stable frequency for homelink to learn.
It's receiver is more frequency sensitive than the garage door opener itself, so if you are having trouble find a good quality or OEM remote to engage.
Fortunately I have a spectrum analyzer and figured this out after way too much time.