It's hard to respond to several questions in a single thread. I'll try though
For 1), there are plenty of reasons to use packaged contribs instead of manually install it in an ibay. Here are a few of these reasons
- Simpler to install. Most of the time, it's a matter of yum install followed by a signal-event and you're done
- There can be a much better integration out-of-the-box. Most, if not all of my webapp contribs are carefuly configured to work with SME without any action. By using SME authentication when it's possible (either basic auth, or with LDAP), by making sure the SME admin user is an admin of the app, by pre-configuring emails, links, database
- By providing simple DB props for the most common settings, so you don't have to mess in the app config to set a bigger file upload limit for example, you just set it from the cmd line (it's usually explained in the wiki)
- It can provide automatic integration with other contribs. For example, all of my webapps contribs can be used with LemonLDAP::NG (a WebSSO)
- It can (and usually does) provide a much higher security level. Installing web application shouldn't be limited to extracting it somewhere and hoping for the best. Yes, it'll usually work, but if you want to hardden it, you have to carefully look at the app to see which folders must be writeable by www, and which should not. This is not really possible in ibays. It's possible in Shared Folders, but still painful. There're also some php tuning which might be needed, and some includes folders which should be denied by the webserver. All of this have to be done manually if you install your app manually. With the packaged RPM, it's already done for you
- It's much much much (much much much) easier to maintain when you have several servers to manage. If you just maintain your own server, yes, you can afford to manually check the app you have installed, and update them manually from time to time. If you manage, say 10 servers or more, it's not desirable. Just yum update, and you're done. So, I disagree with you on this point, it's much easier to update when using a packaged contribs
- For the access path, yes, the contrib does choose the default for you. It's a bit less flexible. But you can create a custom template, or ask as an NFR to set the alias in the DB, so it's easy to change. Or you can use http://wiki.contribs.org/Webapps-common and create the sub-domain you want pointing on your app
For 2), yes, you must be careful with backups, as data won't be automatically backed up with the default tools.
For 3) ibays are more for network shares IMHO. They can be used to serve files through HTTP, but are not the best for this. BTW, you should take a look at the Shared Folders contrib, which work a bit like ibays, but are much more powerful (supports finer grain ACL, webdav, etc..)