Please add the path "/opt/jakarta/tomcat/conf" to CONFIG_PROTECT in /etc/make.globals (this path is used by net-www/tomcat).
In Portage 2.0.18 and greater, you can use this modular approach to do it. Add an /etc/env.d/51tomcat file with this in it: CONFIG_PROTECT="/opt/jakarta/tomcat/conf" CONFIG_PROTECT is now incremental like USE, so old options won't get overwritten. But the long-term solution is to get jakarta's config files in /etc/opt, which is what the FHS tells us to do. Maybe use a symlink and store jakarta config in /etc/opt/tomcat/conf? That's the best solution.
I think >=portage-2.0.18 should be added as a dependency then? That will have to wait until an unmasked version of >=portage-2.0.18 is out then.