I contacted FTMO regarding the use of EAs on both challenges and funded accounts with them, and here is their reply…
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Be informed that EAs are allowed at FTMO.
We do not interfere nor give advice on that, we just want to make sure traders understand the maximum allocation per trader/strategy of 400 000$.
As long as your trading is legitimate, conforms to the real market conditions and we can replicate your trades on our live corporate accounts, there is no limitation to your trading style or strategy. If you intend to use trading robots (Expert Advisors – EAs), keep in mind that if you use an EA from a third party, you run into a risk of being denied the FTMO Account if you exceed the maximum capital allocation rule.