Daniel Nashed commented on this recently. FP9 includes the same SR4 FP5 version of JVM as FP8 does. My suggestion would be to install FP9, bring Domino online, and issue show jvm to confirm that JVM was patched correctly. If it has not (I saw this happening sometimes with FP8), then run the standalone JVM installer. Then start Domino to verify through show jvm at the Domino administration console that JVM is at the correct patch level. A server that I patched last Friday as FP9 had no issue with the JVM, but that is only one server. 

Source: http://blog.nashcom.de/nashcomblog.nsf/dx/notesdomino-9.0.1-feature-pack-9-shipped.htm

So on my servers that are running FP8 with the 'latest' Java security patch here's the results of show JVM: 

Java runtime version: pwa6480sr4fp5-20170421_01 (SR4 FP5)
JVM version: JRE 1.8.0 Windows Server 2012 amd64-64 Compressed References 20170419_344392 (JIT enabled, AOT enabled) J9VM - R28_20170419_1004_B344392 JIT  - tr.r14.java_20170419_344392 GC   - R28_20170419_1004_B344392_CMPRSS J9CL 

That is after installing the Java patch dated 2017.06.12 that was actually released on the 8th Aug 2017! the one referenced by this link Security Bulletin: Multiple Vulnerabilities in the IBM SDK Java Technology Edition affect IBM Domino

After updating to FP9 I'm seeing the same version.  

Tested on a FP6 server and it does upgrade to the same version as the JVM patch.

I agree that the numbering sequence is not straightforward. Also, I would expect that the latest would not be from April 19th, but apparently that is the latest IBM has packaged. The previous one is marked as being from February. 

I don't apply the JVM patch unless the expected version is not displayed after installing the Domino Feature Pack. I would say that applying it usually does no harm, but I've sometimes seen the standalone JVM installation fail. When that happens, I remove and readd the Feature Pack.