Using IspCOnfig3 LE cert on a tomcat application on same server as apache 2.4.x?

Yes, you have to config Tomcat to use the cert.

Yes, definitely.
Have a look a this tutorial: Tutorial - Java KeyStores (JKS) With Let's Encrypt - #6 by ahaw021
And feel free to search the interwebs for other examples, etc.

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