Chosen Solution

Would it be ok to use a 64 gb motherboard in place of original 16 gb motherboard in an iPhone SE 2020?

Yes, and no. Yes you can, but the IMEI# on the tray will not match and Apple will refuse to service the phone in addition to losing TouchID. In addition to that, you need to make sure you buy the right board (Ex: If you have a 16GB Unlocked phone, you need an Unlocked 64GB board). It’s more trouble then it’s worth, since you lose TouchID, True Tone (with no way to recover as you will not have a original paired screen, so you can’t even re-pair it with a established key) and Apple will know. Sell the phone, take the beating and buy a 64GB device with the board from day one factory unlocked - if you can afford it, 128GB.