Apple you need to take ownership of your mistakes. That you owned up to nvidia macbook pro issues eventually and issued mother board replacements was the right thing to do. You have a similar problem here.
I have similar issues (waking from sleep) with a 2012 Mac Mini and using a 4k display (samsung u32d970q).
Although the issues occur at 2560 x 1440 still so I don't think its just 4k that is the issue.
Apple support have tried to blame the display but they are wrong as you will see if you read the post. It's a fault being caused by excessive noise from thunderbolt. I have observed similar interference with thunderbolt devices and different 3 Mac's in the past 2 years, although those issues were not with displays but other thunderbolt peripherals and interference with USB3.
I have logged this issue on https://bugreport.apple.com/
I highly recommend anyone affected by this to log their problem there and post publicly as well for visibility to give us the best collective roadmap towards fixing it.
Anyway here is what I have found through testing-
I have bought a Minidisplay 1.1 to hdmi adaptor and a mini displayport to displayport 1.2 adaptor which has provided useful information for diagnosis.
When converting the thunderbolt port (mini displayport adaptor) to HDMI 1.1 for the display-
in the first test we have issues when waking from sleep. The mac freezes dead in its tracks. When the machine tried to wake (after about 12 hours) it froze.
Also when changing resolutions there was an intermittent issue with usb drives being disconnected.
When converting thunderbolt (mini displayport adaptor) to display port-
The machine freezes intermittently when waking from sleep (usually tested after sleeping overnight after 8 or so hours). The are also issues with usb hard drives being disconnected when the display wakes with this signal.
When plugging the HDMI port of the display directly into the HDMI port of the mac mini-
No issues with sleep! This means the hdmi connection or cable to the screen is not the cause, the hdmi port from the mac is not the cause, and the screen is not the cause since only when plugging any adaptor (displayport or hdmi) into the thunderbolt port is there an issue.
Since the display has no issues with HDMI directly into the mac, the information I have gathered would almost certainly point to this problem being caused by excessive noise / interference from the thunderbolt port. Multiple adaptors and cables have been used so they are not the cause. This is further supported by the fact that the problems occur when the thunderbolt signal is turned off and on (waking from sleep), or the data throughput is changed (resolution) which is usually the point where noise would be at its most from a faulty design during those impulse changes (spikes).
I have observed similar issues before with other thunderbolt devices creating interference on another macs. I have previously seen a thunderbolt cable if too close to a wireless mouse dongle stop it from working in both an imac and a macbook pro. I have also seen an owc thunderbolt dock disconnect all its usb drives plugged into an imac when waking form sleep repeatedly. owc provided refunds for these issues.
Generally any usb plugs that are closer to the thunderbolt plugs are most at risk of this noise affecting them.
There is not a single mac of the 4 mac's I have had in the last 2 years that have not exhibited some strangeness with thunderbolt interference. I hope that apple can use some testing methods to determine the noise from the thunderbolt as being excessive when I can bring in the mac mini for them to test.
I hope apple can take ownership of this thunderbolt issue, there are surely many other users out there without the resources or skills to diagnose a problem in the same way and if they are at the whims of someone not so knowledgable at the end of a phone they are not likely to get a positive outcome.
The only solution I have right now is to disable sleep. On a mac mini thats not so bad, but not good enough.
I have to wait until I get another system to use while this can get tested by Apple.