The PHP time settings might have something to do with it as I think moodle inspects the package to check it is all right and does some other things with it.
However my upload limit is only at 20M and all of my packages are bigger than that. Changing that should make no difference at all if you use a repository as you aren't using the PHP upload method then.
If you are using the values in that link then I would scale back quite a bit. You are giving any PHP script up to 60 minutes (!) to run with those settings. Nothing should ever take that long and is a security risk. I'm currently at 180 and that works just fine. 3 minutes should be more than enough for anything moodle has to do.