Will these parts (graphics card especially) fit into a Bit Fenix Prodigy M case?

It's not compatible due to this (completely bizarre) statement on the Prodigy M page -

Q: Will the XYZ Power Supply or ZYX Video Card fit inside the Prodigy M?
Video cards at 9.5inches or less will have 200mm of power supply clearance
Video cards at 11 inches or less will have 160mm of power supply clearance
Video cards at over 11 inches will have 150mm of power supply clearance.
Basically, you can have either a longer graphics card or a longer PSU but not both.

Aside from that, you have all of the inherant issues which come with the odd layout of the Prodigy M. I've mentioned these before in many posts comparing the ITX and mATX versions so I won't repeat myself (it should be easy to find by search anyway). The TLDR version is that there is very little (if any) advantage to the mATX version because it has greater limits on component selection and a lack of ability to support the advantages of the mATX format.