Just tested this in BC and it is possible.
Maybe You have some kind of localization that changes how entries are posted?
Re-check that the Journal template and Batch has the Allow VAT Difference (I assume this is checked, otherwise You would have error when trying to change VAT Amount).
What I did:
1) Create a line for amount 100, and Balancing account Bank. System calculates 20$ VAT

2) I adjust the VAT Amount to 18$ and post the journal line

3) The result is posted with 18$ VAT
