(version 6.x to be exact), there was an actual physical link between the SEPM and the NS. I found that version to be quite useful, but it had it's limitations. You had to have a one to one link and initially I think you could only have one NS and one SEPM, not useful for large organizations.
However, it read the SEPM database and populated everything off of that. In version 7.0 and going forward, it relies primarily on the task to gather the inventory data, which isn't as useful if not all your system can or don't have the Altiris agent.
The reports and web-view limitations, as you have found, are probably based on internal queries, which most likely won't recognize the latest versions. You could possibly dig into the web-parts and queries and manually update them.
You can still deploy your SEP packages via Altiris, but again, you'll see the limitations you already mentioned. Again, you could build custom filters for your targets.
That being said, most (all?) SEP customers are entitled to and strongly encouraged to use the IT Analytics plug-in\pack for SEP. If you can get it to work (there have been numerous issues), it does the work of the reporting by reading the SEPM directly.
If you have a chance to go to Vision, or even if you don't', see if you can provide the feedback to Symantec (via support, sales, or product managers) to help improve the tool.