as i mentioned in the comment above, it looks like the wtp plugins do not call the startup scripts, but directly call on tomcat through the java executable. therefore, the vm arguments from eclipse are put directly on the command line, not stored in some config file such as setenv.bat, neither does it read from such a config file from startup. therefore the two are completely separate in configuration.
as far as i know, you can not do this in tomcat and should do extra work in eclipse's settings.
if your project is eclipse's dynamic web project, go to menu>runas>runconfiguration and in environment tab, add those parameters that is in setenv.bat. if your project is multi module mavenized project, go to run configuration of that module that has war packaging in pom file and do the settings above mentioned. also, in arguments tab, you can specify program arguments and vm arguments. note: startup.bat runs another bat files that they may set another parameters. if you faced with any error, you may check other bat files.
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