I think that the correct way to store a key pair is to keep complete information about it. There isn't any need to negate if a correct key is given.

A key is manipulated/altered/modified/composited/tweaked independently of the operation of negation described in the BIP340-342.

I think that the quote ("may need to") supports that position: 

> Note that because tweaks are applied to 32-byte public keys, `taproot_tweak_seckey` may need to negate the secret key before applying the tweak.

[https://github.com/bitcoin/bips/blob/master/bip-0341.mediawiki][1]

In other words, above mentioned negating should not be mixed with other operations. Also, the negation is not necessary when you have complete information about keys being used.

  [1]: https://github.com/bitcoin/bips/blob/master/bip-0341.mediawiki