FWIW - we can effectively guarantee our memory compatibility and full Apple spec there for. I apprecite the recent testing done by a couple customers who had experienced past issue where our Memory was in the mix, but have been able to confirm no issue in the present day with current product provided. The Mac mini has it's own challenges likely related to the HD4000 video - even where we don't see similar issues with other HD4000 video equipped 2012 MacBook Pro 13" models.
I will add though that there are a lot of moving pieces. I use currently use a Retina unit that is fully factory (memory factory soldered) and while I've had no issues with my single display and dual display setups at two locations - a location I travel to and use an iMac in display slave mode, just last week this setup had a black/flicker on-off about once every 1-2 hours. I didn't have to restart, the display came back on as quick as it shut off... This was with a 2 Meter Apple Thunderbolt cable and in this case I wonder if just a signal issue?
In the case of the Mac mini, and we're still working to have a unit today (note Apple has continued pushing updates that do impact this issue for all the TB Mac models) where we can get the original reported issue to surface around a memory set. In that case, the report was consistently here with two displays and when the display went black, only a restart would bring it back. FWIW - in 2012, I did see the same kind of issues and lots of general frustration with my Retina as well - although usually the main issues were at initial hot-plug in. Today, things pretty stable.
If your issue is a periodic on/off flicker - I'd look first to the cabling. In the case of mini-Display port adapters especially, we have seen issues corrected by replacing a cheapie with one of our NewerTech or Apple adapters fixing that and other video issues.