You can’t since WP doesn’t know it’s installed. All I create is unique custom themes form clients and I install ACF the standard way. 99% of the time I am the one maintaining the site and doing the updates.
I am a firm believer in not marrying clients and I want them free to move on if they choose to do so, so I don’t hide anything from them.
My suggestion would be to move it into the plugins folder if you’re not going to be maintaining the site. There is nothing wrong with using ACF to create a custom theme.
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