In general, no. You can't have two server processes that share the same jboss.server.base.dir (e.g. $WILDFLY_HOME/standalone by default.) And an embedded server inside a CLI process is effectively a server process.
Now, specifically why what you are doing is causing the non-embedded server process to reload applications, I don't know. Perhaps other users who've done similar things will have an idea why. All sorts of bad things can happen when two processes share the same writable dirs, so we haven't particularly thought through all the various possibilities.
When you say 'applications are reloaded' do you mean the server as a whole reloads? Or just deployments are redeployed? How are they deployed? Via the deployment scanner?