There are some sites that no longer have manuals. I know of at least one Integrad location that swapped out all its manuals and only uses automatics now for the integration station training because some of the centers that feed into it have only automatics.
I personally never gave a road test in anything other than the crappiest manual we had on hand. It was my responsibility to make sure if I passed someone it was because they could handle the hardest vehicle they are likely to face without killing someone. Anyway, I never dealt with the automatic only issue. My guess is the paper you signed will go in your file. The only possible use for it I can think of would be to A) deny you your guarantee if the only route they have for you is in a manual, saying it is work you are not qualified for. Or to B) CYA for themselves in case you wind up in a route in a manual to say "he signed this, he should have known better."
Either way it should be a non issue unless you are asked to take a route out in a manual before you wind up getting certified in one. So under no circumstances drive a manual until you can get certified. If a management person asks you to, refuse, politely, and reference the automatic only certification in your file. Just my 2c from a management perspective.