That's pretty good. I did suggest a Gigabyte motherboard for Thunderbolt 3 support, but after digging, I found out that the motherboard you listed supports Thunderbolt 3, and MSI does make an expansion card for it.
You would need to save the slower PCIe X16 slot for the Thunderbolt 3 card though. The 2nd PCIe x16 only runs at 4x anyway.
Otherwise, it looks like a solid build. Only suggestion I have is to get an ultra quiet PSU and quiet case fans.
Thunderbolt 3 is the ultimate in expansion ports. That being said, a mother with Thunderbolt 3 support will have it baked into the motherboard, so you won't be able to upgrade to Thunderbolt 4 unless MSI does it as a software ugprade. (Which Apple is doing for some of its most current computers.) That being said, about the only real difference is an upgrade to 8k monitor support, and the ability to use a Thunderbolt 4 hub, instead of daisy chaining everything.