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There are lots of reasons. One of them is Thunderbolt 3, yes. But the biggest reason is that AMD processors didn't become viable until very recently. The Mac Pro had been in development for 5 years, there was no way AMD was going to be in it. 

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21 minutes ago, Arika S said:

it doesn't just "run smoothly on intel". thunderbolt  is an Intel property

 

so likely, given how many of Apple's accessories utilize thunderbolt it would cause massive outage

intel released a version of thunderbolt so it's no longer a strictly intel thing, some x570 motherboards have thunderbolt

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17 minutes ago, _d0nut said:

intel released a version of thunderbolt so it's no longer a strictly intel thing, some x570 motherboards have thunderbolt

And they probably pay a lot of money for that privilege too.

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2 minutes ago, Enderman said:

And they probably pay a lot of money for that privilege too.

No. Thunderbolt is royalty-free now.
https://www.guru3d.com/news-story/intel-releases-thunderbolt-to-the-industry.html

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