Benefit of loading JavaScript in template.php rather than the theme info file?
No real advantages. 

There are two reasons to add Javascript : to make some elements work, or to make them look cool. 

JS to make something work

These should be #attached to the element they make work. Preferably in the module that created said element. Or they may be written in unobtrusive way and put in info file of this module. Either way, they should never be put in theme, makes no sense to have them there. So these should be out of your question's scope. 

Eye candy

These belong to theme all right. And because they do, they shouldn't depend on any script that's in module. If you have a rare situation when they do, then you need to add them in PHP for conditionals that'll cache and not waste browser's resources. But you told no conditions, so this is moot. Or should be, if your theme just assumes presence of modules without checking you have serious bug there, problems waiting to happen. 

Having them added in PHP allows some reordering etc. In my experience it was always easier to write my JS in a way that didn't require this. Drupal Behaviors are good for this. If for some reason you can't write your scripts in order independent way, ie you have to use external scripts or have no time for rewrite, then #attached is the way to go. 

Other "advantage" would be to attach them only to elements that are supposed to get their cool effects. But this rarely is an advantage. If all you need is to make sure JS is included, include it always. Better for caching and it'll act only on elements with specific id or class anyway, no real harm for browser. Exception here is when you need to take some php variables and make them avaliable to Javascript. Then info file will obviously not suffice and you need to add it via php.

TL;DR

Your intuition is generally good.