Well obviously the iems are going to be more portable, and depending on the tips they will probably have equal or more isolation. Personally for comfort I've never liked iems which is why I go for portable headphones when I'm on the go.
As for sound, can't say I've ever heard the se846's but most people seem to think they're excellent. Would probably be better than the pm-3 (and at over double the cost I should hope so!)
Don't think of price as a linear progression. Certain companies throw things out happy to make a penny on every pound, some prefer to take care of their image, others have amazing mass production skills that net savings down the line and they thrive on that model. The only time it is fair to compare price is between two equally set up competitors, or better yet, between models in a company's own line. Otherwise, it is pointless.
The PM-3 is a bargain on all fronts: well made, easy to use, great machine quality, attention to detail that goes far beyond everything on the market, great branding, and good-to-great sound. The SE846 isn't as strong on the branding, but on the engineering front it is one of the most appealing products I've ever tested.
You can read my thoughts here. Of course, if its sound isn't to your liking, it won't tickle you. I tend to prefer a more exciting sound, so getting used to the SE846 (and the PM-3,
which I reviewed here) took time. But love both I do. And, in the end, I purchased a PM-3. The SE846 has one problem that kept me from purchase: comfort, which is only good but not great. Comfort for me is the most important thing, followed by ease of use. It's a given that hi-end headphones from reliable manufacturers and sold to audiophiles are going to sound good. So that is a given, and is last in importance to me. I expect it to sound good. If it doesn't even do that, chances are that it is great on other fronts are nill.
