PopupAlly Pro can work with MailPoet with partial functionality. Since MailPoet does not provide thank-you page redirect, it will not show thank-you page after the opt-in is submitted.
Also, the thank-you popup does not work properly with MailPoet (subscribers cannot be added in MailPoet if the thank-you popup is set). Nor does the thank-you page stopping popup mechanism.
Please be careful when using Mailpoet as it is limited in functionality. We do have many other programs we integrate with if you need full functionality.