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No. Google pay will not work with MIUI if you have an unlocked bootloader. I just ran into this issue and contacted google support.
Their official response is as follows:

"
I had escalated your case to our specialist team, I have received an updated. Our specialist found that your device bootloader is unlocked. I request you to please have the device bootloader locked. In order to use the Google pay app for the in-store purchase, the bootloader of the device needs to be blocked and also should have the NFC enabled on the device. Also make sure the Google pay is set as a default payment app. Please contact the device manufacturer to have the bootloader locked.

"

So in order to use Google Pay we either have to able to find a way to relock the bootload while keeping the system functional, or find a way to block google from detecting the unlocked bootloader.
 
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My guess is that the kernel doesn't block that information (the state of the bootloader) and thus Google ends getting it, despite using Magisk. I have only found this issue over new terminals (I have a Mi 9). I think we'll need to wait until a custom kernel its developed, so the kernel its able to block that information from any Google app. This is basically what LineageOS does for example, but any ROM with a custom kernel should theoretically work as well.
 
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I chewed google's ass over it.

They would rather have you running a chinese rom full of bloat/spy/adware with a locked blootloader, vs running a clean, safe, and adfree rom with an unlocked bootloader.

Flawed logic.