Are there any downsides to prefixing my HTML documents with
<!DOCTYPE html>
Will it break compatibility anywhere significant?
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It will not.
This doctype was chosen for HTML5 because it is the bare minimum required to invoke standards mode in browsers that care about such things. Provided your markup is standards compliant you should not have any issues.
Browsers that don’t care about the doctype will just do what they’ve always done.
Edit: Here is an overview of the different modes, and the impact this has on different browsers.