Startup options conflict?

We are migrating from ES-2.3 to ES-5.4.0 and I am updating chef infrastructure code to accommodate both versions. When I install 2.3 to Ubuntu hosts, we have it configured to run as a daemon, using some boilerplate config files with app-specific settings.
I've noticed that when I install 5.4.0, it writes a jvm.options file that may be conflicting with some environment variables being set in our daemon-config. My question is, if I split those jvm settings out of our config and use the /config/jvm.options, is it picked up automatically? As it is, I am not able to get the app started at this time, but not getting anything logged to point out what's causing the thrashing.

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