Mike,

You can do 2 things

1 - Log a ticket with support regarding a defect in the installer not recognizing your version properly

2 - You don't 'need' to run the installer, really all you need to do now that you have a fully functional Tomcat, is get Mid-Tier into it....this is easy enough to do.....download the war file...name it arsys.war and put it into the Tomcat webapps directory, Tomcat will take care of unpacking the war file and all you need to do at that point is configure it.  There are a few other ways to do it, but all of them are more complicated....if you don't want Tomcat to control the deploy via war...you can extract the war (just a zip file) and put the extracted folder inside webapps.

Yes a standalone Tomcat (or JBoss, or WebSphere, or ServletExec) is supported. It is actually the best practice for many of the reasons you mentioned, however I don't remember if it is officially documented at such. In conversations with product management over the years they have mentioned that Tomcat is shipped with the product more for quick non-production/proof of concept systems. They want a usable product out of the box without you needing to go and download/install/configure a separate servlet engine and then deploy MT.

You can check the BMC Product Availability and Compatibility Utility to see which JSP containers (aka servlet engines) are supported.

You are correct though that the installer does not always place nicely with an existing servlet engine, that was not installed by a BMC installer. I think I haven't had an issue with the 9.1 installers but in prior to that (maybe pre 9.0) often the installer would not see my existing Tomcat or complain about the version (I think partly because it did not correctly identify it). From there the installation prompts are a little awkward.

More often than not I use one of the methods LJ LongWing mentioned. Over time I found it kind of silly to "install" Mid Tier since it is a web app that is deployed in a web app server.

The other benefit of handling the deployment of MT your self is you can have multiple versions. I often will stop TC, rename the the 'midtier' directory (include the version number so I can easily tell the version later) and then unzip the .war files as 'midtier'. I know some people copy the old config.properties files but I like to get any update BMC provided (same with custom login.jsp pages) so I will update those by hand or later in the web UI after starting TC. If you need to switch back to the prior version for any reason stop TC, rename the current 'midtier' dir (include the version number) and rename the old copy of 'midtier_nnnnnn' to 'midtier' and start TC. You are now back to running the previous version of MT.

Yes, you can certainly keep Mid-Tier in it's own folder....as i said, that just complicates things a bit....that requires putting a file in the conf\Catalina\localhost folder...typically named arsys.xml pointing to the location of the 'external' mid-tier....not difficult in any way, just more complicated...:)

Another reason to install your own version of Tomcat is to get past the security vulnerabilities identified with the version of Tomcat bundled with the MT Installer. (Thanks to BMC for the foresight to make this possible and supported) We had a number of projects last year where our customers wanted to eliminate security vulnerabilities including those that come with Tomcat, so that forces you to use the latest and greatest version of Tomcat, as the resolution of some vulnerabilities require a version upgrade of Tomcat.