In that case, I suspect you have an acceptance curve to navigate. The in-app Gantt is orders of magnitude better than it used to be, but it is still a long way from the functionality offered by MS Project (not to mention the "known" user interface, etc.).
You're right, the integration is a long way from "seamless", but I'd still advocate it for larger projects. Personally, I prefer Open Workbench to MS Project (that's possibly my subversive nature!) but again, there's a learning curve for your PMs to go through if you're going to go down that road.
I'm not sure I agree about the 100-line comment, especially if you're going to use templates as a starting-point. I've used the in-app Gantt for projects of ~250 lines, and although it's a pain to establish it, it's fine for on-going maintenance and re-planning. I wouldn't, however, want to use it for anything large (~1000 lines or more).