Of the millions of transistors in a typical microprocessor, what percentage of them are BJTs and MOFSETS?
In a microprocessor: ZERO. All modern processors use CMOS logic.

Reasons why:


CMOS transistors can be made much-much smaller than BJTs, that means cheaper chips and more functionality per chip
CMOS logic is much more power efficient than logic made with BJTs
When CMOS logic is static (no state changes like when in standby) current consumption can be almost zero. This is impossible to do with BJT based logic.
CMOS manufacturing processes are generally simpler (less processing steps) than processes with BJTs. This means lower manufacturing costs.
If your Iphone used BJT based logic for everything then it would need to be as large as a truck, half of which would need to be reserved for the battery or generator and fuel.


BJTs are often used in high frequency circuits like the circuits that connect to the antennas. There is a trend to use CMOS transistors for this as well so what is used depends on price and what performance is needed.

What is used in a particular phone can only be answered by the designers or you'd need to reverse engineer the phone. You would need a well equipped lab to do that and specialists to analyze the chips. Many chips will be unmarked and even if you would know the model number of a chip then it might not be clear if it uses any BJTs inside.