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This restriction is in place for security reasons. Allowing PHP scripts would make it too easy for internet criminals to abuse Yola to create malicious sites. Unfortunately we need to protect ourselves from this in order to continue to offer our service.
I had this problem too, but have to admit that Yola makes our life so easy that now my company website is up and running. But, as a Yola user, I believe there will not be any internet criminals among us. If there are, I believe Yola will protect themselves and their users/customers as well, human nature :-) I have to make a suggestion, since restrictions of .html and .php files makes a bit frustrations for the users, who are dying and willing to put more features to their sites made through Yola. But, since this is all because of internet criminals, I believe there could be someway to stop this and allow other Yola users with the missing feature. (eg: like paying Yola to use the missing feature or becoming a Pro member etc).
I apologize for the inconvenience, but since I am a Yola addict, I would like to make such a suggestion, just to make sure that the Yola team would think about this and inform the non-criminals like us the happy news, if there is going to be a happy news :-D