Ok, I can confirm the above observations that the widgets do apply with synthesis scanners when Helios is using them and that it doesn't generate Simaris standing.

I can also confirm that Helios likes to preferentially use Codex scanners first and that affinity is generated when doing so. I cannot confirm whether Helios scans with widgeted synthesis scanners generate affinity (I forgot to track when I ran out of codex scanners).