Hmm, the code in MooseX::Traits states ...

Not sure who wrote that comment, I suspect either Florian or Jonathan Rockway, I would not take that too much to heart, it is an opinion and a somewhat extreme one at that. It also may very well refer to an earlier state of that behavior, a lot of cleanup has taken place in that corner of the code base in the last few years.

So why should I be scared of Trait->meta->apply?

You shouldn't, but some people are scared off by the MOP (which is a good thing sometimes and a bad thing other times).

Why would writing it myself be better than the function that appears here?

Well, what is in MooseX::Traits has already been tested and is regularly tested against the Moose core with our smoke tester. But the code is basically just calls to Moose::Util functions, so I wouldn't worry about writing your own code too much.