There are a few significant differences in the 3 and the 6, but none that would affect the delivery of the methanol to the motor. The differences are:

The 6 has an IDC trim function for scaling the jetting
The 6 has adjustable boost pressure compensation, if enabled, the 3's is fixed
The 6 has a dedicated MAC valve circuit for wategate actuation, the 3 uses the standard failsafe contacts
The 6 has an adjustable failsafe reset timer
There are a number of more minor items the 6 employs.

Again, these are features that are above and beyond the basic operational functions that both share. You will get the same basic functionality and power from either system.

If you get to the max airflow of the stock turbo and need more from it then the pre-turbo sprayer can help, or if you live in an very hot and dry climate it could help as well. The closer to stock the powertrain is the less effect the pre-tubro sprayer is likely to have.