Right now, I have a link defined as such:
<a>itms-services://?action=download-manifest&url=https://loqi.me/install/Geoloqi.plist"</a>;
When a user clicks on this link, the following message is shown:
The message consists of the domain-name where the .ipa resides and the application name as defined in the plist. Is it possible to change this prompt message?
Try
https://developer.apple.com/library/ios/documentation/General/Reference/InfoPlistKeyReference/Articles/AboutInformationPropertyListFiles.html#//apple_ref/doc/uid/TP40009254-SW1
The short answer: No. That is not possible.
And it actually makes allot of sense. Since enterprise apps does not go though any app review it is fairly simple to make an app that's spy on the user or steal data. With the current system the user at least get information about the domain/publisher of the app.
Consider such an "evil" app signed with a valid enterprise license identifying itself as "Important update from Apple" or something similar...