POP3-MAPI-application sending/receiving mail

I plan to migrate client to exchange 2016 and client wants me to disable POP3,IMAP on a new mail server.
That is not a problem but what about applications.Some applications require POP3 protocol as incoming and not MAPI.
For example jira

"Yes, enable standard POP or IMAP on the Exchange server. (Ideally IMAPS for security) MAPI is not supported because it's proprietary and expensive.It is possible to build an add-on, but you'll need to pay Microsoft for the rights to use the protocol in your code. That's why Atlassian hasn't done it, it costs too much."

Is there any workaround for this  problem?
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Mohammad Ishtyaq khatriSr. Systems EngineerCommented:
Few suggestions: You can control this settings on the mailbox level if you don't want to do it on the server level. OR you can setup a different mail service just for pop\imap and have the routing to your production mail servers.

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