Completely off the top of my head and untested ...
Have a 2nd email smart campaign with smartlist that selects the original list and filters to those with non-blank alternate email field.
Then, the Flow would first swap the alternate email field and the Email Address, send the email, swap them back. You probably need a 3rd field to hold the main email address.
temp_email <-- Email Address
Email Address <-- Alternate Address
Send the email
Email Address <-- temp_email
maybe you need a couple of Wait steps to let the values update?
And maybe you need multiple campaigns one to temp change Email Address, one to send, one to reset the Email Address?
Worth the experiment 😉
Probably pretty dangerous
If the lead comes to a web page and fills out a form with the first email address while the second is in the email field, Marketo will create a second lead...
The send alert should work if you i,nsert the token in the "Other" field of the send alert flow step.