The issue you can run into in practice is stuff like softsubbed signs, which can clash and look out of place with the native video if you render them at full res. There's also a related issue, which is that if you're using something like motion interpolation (e.g. “smoothmotion”, “fluidmotion” etc. or even stuff like MVTools/SVP), softsubbed signs will not match the video during pans etc., making them stutter and look very out-of-place - the only way to fix that is to render them on top of the video before applying the relevant motion interpolation algorithms.
Personally I've always wished for a world in which subtitles are split into two files, one for dialogue and for signs, with an ability to distinguish between the two. (Heck, I think softsubbed signs should just be separate transparent video streams that are overlayed on top of the native picture, allowing you to essentially hardsub signs while still being capable of disabling them)
Also, sometimes, rendering at full resolution is prohibitively expensive, e.g. watching heavily softsubbed 720p content on a 4K screen.
Sure, you have to transform the coordinates to the output. But still, better to render fonts at the final resolution; they'll always look better than if scaled after rendering.
The font will look better but you have zero guarantee that the subtitles will be better too. Furthermore, you will lose any artistic value that the creator intended.
For example, go get the Russian movie Night Watch and watch it with the original subtitles hardcoded and as a separate file. The director insisted on doing the subtitles himself and he used them for great artistic effect throughout the movie [1]. Watch it with scaling and aspect ratio stretching to see how nicely rendered, crisp high resolution fonts can be inferior to a pixelated, stretched version created with intent by an artist.
[1] http://readingsounds.net/wp-content/uploads/2015/12/NightWat...