Okay, so after some research and a look at the MSi board's manual (which has a nifty diagram to explain the different configurations) I can safely say you're good to go with the build you've planned.
PCPartPicker is partly right; Using one or both of the M.2 slots will negate the use of one or two SATA3 ports, respectively. However, this only applies if you were to plug in an M.2 compatible SATA SSD.
NVMe (or PCIe) SSDs like the 960 EVO you've chosen utilise the much faster PCIe lanes. A similar bandwidth sacrifice will be made, but instead with the last PCIe lane on the motherboard, which is scarcely used anyway.
This also means that you can use BOTH M.2 slots populated with 960 EVOs and ALL 6 SATA3 ports.
Check the manual out yourself if you'd like to verify my understanding:
https://www.msi.com/Motherboard/support/X370-XPOWER-GAMING-TITANIUM#down-manual
Enjoy! Beast setup btw