There's really no way to 'emulate' Alpha-ROM with Daemon-Tools right now. Alpha-ROM isn't emulated. The cd is distinguished only by the ability of reading the data in the protected area. Removing the protection means to replace the protected area with normal data extracted from the area.
It's an agressive protection scheme. Although Settec claims that 99% of current cd drives are compatible, some speculate that a higher percentage of drives are incompatible with it.
After many people complained that the protection was incompatible with their cd drives, TYPE-MOON(A game company in JP) now offers to send a non-Alpha-ROM version(but tied to one main hardware configuration) of its newest game to people who can verify their leagal ownership of the game. Perhaps the company of the game you want to copy has something similar to that too.
If not, there are two things you can do. You can remove the protection by repairing the cd image manually/automatically by some software or by making a cd image without the protection with an Alpha-ROM compatible imaging software. Or you can get a no-cd ***** for the software.
You might be able to get an image of the game with the Alpha-ROM protection already removed through the internet...not that I'm suggesting it.
...or at least I think those are about the only thing you can do to make/get a good image of an Alpha-ROM protected game. And again, I don't say this is absolute, since I don't own an Alpha-ROM protected game.