Great Question!
Intuitively, you are right, minification of assets should be performed on application Startup. You assume that assets are delivered identically to all browsers. But Microsoft believes that much of JS and CSS is browser specific.
If you check asp.net site's reference on ASP.NET 4.5 Bundling and Minification, they specifically state:
Bundling and minification in ASP.NET 4.5 is performed at runtime, so
that the process can identify the user agent (for example IE, Mozilla,
etc) , and thus, improve the compression by targeting the user browser
(for instance, removing stuff that is Mozilla specific when the
request comes from IE).
:
What about caching?
Bundling isn't as obtuse as a profiled would have you think. If you look up MVC 4 Bundling and Minification reference, they point out:
Bundle Caching
Bundles set the HTTP Expires Header one year from when the bundle is
created. If you navigate to a previously viewed page, Fiddler shows IE
does not make a conditional request for the bundle, that is, there are
no HTTP GET requests from IE for the bundles and no HTTP 304 responses
from the server.
This is far more information than you need, but the message is that, JSMinify has a check for relevant cached minified assets.
When you factor in further that we already use minified version of our assets (eg jquery.min.js, jquery-ui.min.js), you can appreciate that .Net minification is a supplemental process.
Why does Minification of all types have to happen