I purchased 10 of the mid tier Mac Mini's last year for a campus expansion at my previous employer as well as for new workstations at my fathers business. Unboxed them and installed new Samsung and Crucial SSD's in each one of them first thing. Didn't even boot them up till the SSD was installed and installed fresh copies of Sierra via USB installer. Worked like a charm and it was much cheaper going with third party SATA SSD's (256 and 512GB models) than Apple's options by a long shot.
After the first few I was getting them swapped in around 10 minutes a piece.
iFixit's guide is excellent here.
Personally that's what I would do in your situation, but it won't help the issue of the Haswell era Iris Pro being stuck with 4K 30Hz. Same as my 2013 13" rMBP. I just continue to use an older 1080p panel and will probably do so for another few years at least. I tend to go about 7 years between Mac purchases.
I should add that two of them were the base models and even those are pretty snappy with the SSD, but limited to 4GB of RAM. Fine for the front desk/office users that just use a web browser, Mail app, and Office 2016 apps for the most part.