Commenting out the options in the stock jvm.options and setting doesn't work:
$ docker run -it -e "ES_JAVA_OPTS=-Xms512m -Xms512m" docker.elastic.co/elasticsearch/elasticsearch:6.6.0 bash -c "sed -i'' '/^-Xm\(s\|x\)/s/^/#/' /usr/share/elasticsearch/config/jvm.options && /usr/local/bin/docker-entrypoint.sh eswrapper"
OpenJDK 64-Bit Server VM warning: Option UseConcMarkSweepGC was deprecated in version 9.0 and will likely be removed in a future release.
[2019-05-17T01:43:49,043][INFO ][o.e.e.NodeEnvironment ] [pWjpdwD] using [1] data paths, mounts [[/ (overlay)]], net usable_space [9.1gb], net total_space [87.7gb], types [overlay]
[2019-05-17T01:43:49,053][INFO ][o.e.e.NodeEnvironment ] [pWjpdwD] heap size [1.2gb], compressed ordinary object pointers [true]
[2019-05-17T01:43:49,063][INFO ][o.e.n.Node ] [pWjpdwD] node name derived from node ID [pWjpdwDgSji5LV5k6QxrrQ]; set [node.name] to override
[2019-05-17T01:43:49,069][INFO ][o.e.n.Node ] [pWjpdwD] version[6.6.0], pid[9], build[default/tar/a9861f4/2019-01-24T11:27:09.439740Z], OS[Linux/4.9.125-linuxkit/amd64], JVM[Oracle Corporation/OpenJDK 64-Bit Server VM/11.0.1/11.0.1+13]
[2019-05-17T01:43:49,069][INFO ][o.e.n.Node ] [pWjpdwD] JVM arguments [-XX:+UseConcMarkSweepGC, -XX:CMSInitiatingOccupancyFraction=75, -XX:+UseCMSInitiatingOccupancyOnly, -Des.networkaddress.cache.ttl=60, -Des.networkaddress.cache.negative.ttl=10, -XX:+AlwaysPreTouch, -Xss1m, -Djava.awt.headless=true, -Dfile.encoding=UTF-8, -Djna.nosys=true, -XX:-OmitStackTraceInFastThrow, -Dio.netty.noUnsafe=true, -Dio.netty.noKeySetOptimization=true, -Dio.netty.recycler.maxCapacityPerThread=0, -Dlog4j.shutdownHookEnabled=false, -Dlog4j2.disable.jmx=true, -Djava.io.tmpdir=/tmp/elasticsearch-10833520116017359688, -XX:+HeapDumpOnOutOfMemoryError, -XX:HeapDumpPath=data, -XX:ErrorFile=logs/hs_err_pid%p.log, -Xlog:gc*,gc+age=trace,safepoint:file=logs/gc.log:utctime,pid,tags:filecount=32,filesize=64m, -Djava.locale.providers=COMPAT, -XX:UseAVX=2, -Des.cgroups.hierarchy.override=/, -Xms512m, -Xms512m, -Des.path.home=/usr/share/elasticsearch, -Des.path.conf=/usr/share/elasticsearch/config, -Des.distribution.flavor=default, -Des.distribution.type=tar]
[2019-05-17T01:43:52,513][INFO ][o.e.p.PluginsService ] [pWjpdwD] loaded module [aggs-matrix-stats]
...
[2019-05-17T01:44:01,666][INFO ][o.e.x.s.a.s.FileRolesStore] [pWjpdwD] parsed [0] roles from file [/usr/share/elasticsearch/config/roles.yml]
[2019-05-17T01:44:02,722][INFO ][o.e.x.m.p.l.CppLogMessageHandler] [pWjpdwD] [controller/75] [Main.cc@109] controller (64 bit): Version 6.6.0 (Build bbb4919f4d17a5) Copyright (c) 2019 Elasticsearch BV
[2019-05-17T01:44:04,042][INFO ][o.e.d.DiscoveryModule ] [pWjpdwD] using discovery type [zen] and host providers [settings]
[2019-05-17T01:44:05,685][INFO ][o.e.n.Node ] [pWjpdwD] initialized
[2019-05-17T01:44:05,686][INFO ][o.e.n.Node ] [pWjpdwD] starting ...
[2019-05-17T01:44:05,979][INFO ][o.e.t.TransportService ] [pWjpdwD] publish_address {172.17.0.3:9300}, bound_addresses {0.0.0.0:9300}
[2019-05-17T01:44:06,029][INFO ][o.e.b.BootstrapChecks ] [pWjpdwD] bound or publishing to a non-loopback address, enforcing bootstrap checks
ERROR: [1] bootstrap checks failed
[1]: initial heap size [536870912] not equal to maximum heap size [1298137088]; this can cause resize pauses and prevents mlockall from locking the entire heap
[2019-05-17T01:44:06,061][INFO ][o.e.n.Node ] [pWjpdwD] stopping ...
[2019-05-17T01:44:06,085][INFO ][o.e.n.Node ] [pWjpdwD] stopped
[2019-05-17T01:44:06,088][INFO ][o.e.n.Node ] [pWjpdwD] closing ...
[2019-05-17T01:44:06,121][INFO ][o.e.n.Node ] [pWjpdwD] closed
[2019-05-17T01:44:06,125][INFO ][o.e.x.m.p.NativeController] [pWjpdwD] Native controller process has stopped - no new native processes can be started