If you're "baking in" parts of Modernizr into your codebase, it seems to me you're still maintaining 90 forks, but it's more work and the provenance of the forked code is less clear.
Suppose you're baking a cake, but it's a custom cake and you're not 100% sure you have the best recipe for frosting.
Suppose Modernizr were a book, and each feature Modernizr tests for was a recipe. What I'm suggesting is this: Instead of going to the library and checking out the entire recipe book just to refer to the icing recipe, just copy out the list of ingredients and leave the book on the shelf. you're customizing the recipe anyway, so if you just add their list of ingredients to the steps you're writing for your own customized icing it's going to be easier in the future than if you write your recipe steps with a little note that says: 'refer to ingredients on page 24 of Modernizr Cookbook'. I also think buying a personal copy of the book for the same purpose is overkill - it makes more sense just to list the specific ingredients you want to reference directly inside the new recipe you are writing and keep it all on the same page, plus not have to worry about where that recipe book is every time you want to whip up a new batch of icing.
How is generating a customized Modernizr build with just the tests you need equivalent to checking out an entire recipe book for one recipe? Either way, you are just getting the tests you need.
Suppose Modernizr were a book, and each feature Modernizr tests for was a recipe. What I'm suggesting is this: Instead of going to the library and checking out the entire recipe book just to refer to the icing recipe, just copy out the list of ingredients and leave the book on the shelf. you're customizing the recipe anyway, so if you just add their list of ingredients to the steps you're writing for your own customized icing it's going to be easier in the future than if you write your recipe steps with a little note that says: 'refer to ingredients on page 24 of Modernizr Cookbook'. I also think buying a personal copy of the book for the same purpose is overkill - it makes more sense just to list the specific ingredients you want to reference directly inside the new recipe you are writing and keep it all on the same page, plus not have to worry about where that recipe book is every time you want to whip up a new batch of icing.