To be fair I can see the problem with strong magnets as they're going to cause a problem if they attach themselves to the inside of a sorting machine, it's things like not being able to send a Li-Ion phone battery on it's own but it's fine to send it in the phone that get me as it makes returning things a pain.
The battery in a phone though is protected by the design of the phone itself (which will be tough enough to stop a fair bit of damage from reaching the battery).
Li-ions outside the phone could be sent in a plain envelop, or whatever leaving them very vulnerable to damage during transit/sorting - never under estimate the stupidity and lack of thought people show when sending stuff through the post*.
IIRC Li-ions can be sent outside the phone or whatever, but much be in something like retail packaging or a suitable container that protects them and does not allow them to short circuit (IE a plastic box, not just thrown in a jiffy bag as I've seen some).
On a related note, I've spotted at least one big name battery manufacturer now seems to have their nimh/low discharge batteries available in a "battery case"** package for the same price as their normal retail package, which I suspect is partly promotional (as it lets you store the spare batteries easily/safely between uses), but could also be a reaction to the restrictions on batteries as I suspect the cases suitable for postal transport.
*There have been issues in the past in MM due to people not thinking about how they package goods they've sold...
**The sort that holds 4 AA/AAA's in a case a little like SD card cases, you can buy them separately (I've been using them for years, ever since I almost had a couple of rechargable batteries I'd got in my pocket go up in smoke when without thinking I dropped my keys into it

