I have to ask, because I really haven’t read that one before. You have some insights or official Google claim for that one?
(Although we do recommend using valid HTML, it’s not likely to be a factor in how Google crawls and indexes your site.)
Source:
For any invalid HTML code, you would get an report at Google Search Console to fix it. Either for SEO meaning (using JSON-LD, etc.).
As far as I use Cloudflare for enough time, haven’t had any error or specific one due to any invalid HTML because or the Rocket Loader at my Websites at Google Search Console.
I am afraid that in case you want to have W3C valid HTML (not CSS) Website, you would need to disable the Rocket Loader at Cloudflare dashboard.
Or, if there is a way to configure for specific user-agent that W3C HTML validation tool uses, to make Rocket Loader “skip” being enabled (not sure if possible)?
- I remember there were some things to go around using PHP
if{}...
, but for some other stuff (not for Cloudflare)
From my perspective as a web enthusiast since being a 3rd grade of primary school, it doesn’t really matter if the Rocket Loader code doesn’t validate. Validation is only a guide, to warn you if there are potential problems in your code due to different presentation at different browsers and users.
You/we would end up at the same “invalidation HTML” even when we use Facebook code at our Website (be it tracking, be it comment/like box, etc.).
If you plan to speed up your website, and use Cloudflare’s Rocket Loader which just doesn’t validate as far for now, so if you are going to use it, you and all of us have to accept that one 
I believe there are no prizes for a clean validation, anyhow - or just having an W3C HTML valid logo?
The tool itself it’s just a way of checking if there are any major issues that may cause your page to break.
- the other thing is if Rocket Loader conflicts with some other scripts and breaks your website …
Moreover, if concerned about SEO, validation of Javascript is not really an SEO issue.
There is also an video here (yes, 10 years old but …):
Don’t optimise for search engines - optimise for humans 