What happens when the e-mail address is decoded with an "E E" when it should have been an "I"? The e-mail bounces and is never delivered.
At a minimum you should have some sort of error checking for the e-mail address. Perhaps send it twice and have the computer keep asking for a repeat until it agrees both times.
The software would play back the email address before sending. If you hear an error, you correct the email address and have it repeat again, and correct errors, repeat again... as many times as necessary until perfect. Then you instruct the software to hit the send button. You could also have the software remember your call sign and use an address book, remember custom user settings, etc.
I haven't used fldigi, but unless it is way head and shoulders above any other CW decoder software I think you are being over optimistic. The decoders I've tried over the years do a great job of copying machine sent code from the W1AW broadcasts but hand generated code takes a lot of interpretation. Computers generally aren't too good at interpreting the context of the message. Try connecting the output of a keyer to your sound card and see how it does when you hand send code. If you are like me you'll be surprised at how bad your spacing looks to a computer. That's a best case scenario too because there is no atmospheric noise or QRM.
Fldigi isn't particularly impressive, but you understand what the ops in a QSO are saying, which is the main concern. You're right about the bad spacing, but that shouldn't make an email unintelligible.
As for noise and interference, that could be a serious problem. Users will just need to make sure propagation conditions are adequate for the station they're trying to contact. Same as with Winlink.