I anticipate, broadly speaking, that a modded scenario made for the 1126B version standard map will work to a reasonable extent in the 1128 version thereof (which omits the various off map changes, and adds new things in previously vacant data lines in the locations file, as I understand it).
As a result, units should appear in the correct places, and the AI scripts should reference the correct geographical locations. However, I have not studied the locations file in detail- this is more of an inference from that which Andrew Brown has said in repect of the 1128 map. Some things might be a little off, and the AI might not be scripted (seeing as a mod generally uses old scripts imported to the mod from the base scenario it was modded from) to use the new dot-locations to best effect.
TL:DR version - I think they'll work because/if the major bases have the same location file line numbers, but I could be wrong.
Edit: As long as Andrew put Aden back in the slot it used to be in before Suez City was added. If not, all bets are off.