No, it's not safe, I just told you that Nintendo technically have ways to easily identify an installed title that does not come from the eshop.
There is no point in saying something is "safer", either it is safe or it isn't, for all you know they might come around tomorrow and start banning people using "non genuine" installed titles, hell they could be building a db for their next ban wave as we speak.
The truth is, as of today, until they add built-in APIs in FIRM to identify a running cfw (or a "non genuine" title) on an offline basis (yes they can do that with a fw update, gw folks just can't spot everything, sky3ds users are even in more trouble if let's say nintendo installs an offline database of "undesirable headers") the only way you can be "safe" is using your own dumps with the original headers dumped from your card.
By the way if you think that can't be done, Microsoft had a similar system in place on the Xbox360 to identify/flag consoles that were running backup or a modified kernel (with hashes checked in some areas of memory at runtime) even as they were disconnected from the xbox live. As soon as the console connected back to the Xbox Live servers, it reported its status, including the flag, which was stored safely in Microsoft's server for their next ban wave.
Let's just see the facts and not to speculate. Nintendo technically can do a lot of things