Hi Kostas,
If you wish to get rich performance and availability metrics of web servers, you may use APM for WebServer but for standard monitoring of your application, java agent is good enough.
Yes since APM for WebServer is an extensions, it will provide you additional metrics which standard java agent cannot suc as availability of webserver, worker process status, I/O, etc. These metrics may vary depending on webserver type. You may go through "APM for WebServer" bookshelf for more details.
Regarding use of Agent profile file, if you wish to use same set of PBDs and rely on auto agent naming, you may share same "InroscopeAgent.profile" file amongst different instances of tomcat but if you are planning to give a custom name to all your tomcat instances, you may use multiple agent profiles. Eg.
IntroscopeAgentA.profile
IntroscopeAgentB.profile
IntroscopeagentX.profile
Hope this answers your questions.
Regards,
Mukesh Singh