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Domino V12 will introduce the CertMgr, which not only supports Let's Encrypt but also manual certificate operations. The internal storage is PEM inside a domain wide new database certstore.nsf.
Most of the functionality is already public in the Domino V12 Early Access Code drops.
There are plans to support export and import for other formats for V12.
Flagging this idea as unlikely to implement because plans are different from what is proposed.
For security reasons Domino is going to keep its own key ring file instead of just trusting the operating system.