MacBook Pro 13″ 2016 – How to set up dual monitors

The Apple mini-DisplayPort to VGA or HDMI adapter terminates the Thunderbolt chain where it is connected, so until Apple released new MacBook Pro with two Thunderbolt ports (similar to the iMac that has two ports) then you will only get one video signal from the device through the Thunderbolt port.

You may find an inexpensive USB to VGA solution to get around this limitation. Initially they were slower, but the newer ones are getting much faster and the software much better. You can then put the most important content on the Thunderbolt port and have the secondary display served over USB.

Should a Thunderbolt adapter come about that drives two displays, I'll update the answer, but nothing has been released (or even rumored) even though it's clearly something the protocol could support.

I like this knowledge base article for the clear deprecation of which Macs support two Thunderbolt displays and which ones only support one.

• Apple Thunderbolt Display (27-inch): Connection options for Thunderbolt Macs

You can indeed use both the HDMI and Thunderbolt ports to drive two separate monitors with a Mac Mini.

Any Mac with a Thunderbolt port can use any mini Displayport display, cable or adapter, so you're correct that the mDP to DVI adapter is what you need¹. If you have a display that requires dual-link DVI (typically only monitors with resolutions higher than 1920x1200), you'll need an active mDP to dual-link DVI adapter.

For the HDMI port, HDMI to DVI adapters are readily available (HDMI is essentially a superset of DVI with a different connector). Note that the HDMI port is limited to monitors with 1920x1200 or lower resolution.

_{¹ Note that the reverse is not true - Thunderbolt monitors can't be used with mDP equipped Macs.}