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_seckeymay need to negate the secret key before applying the tweak.
https://github.com/bitcoin/bips/blob/master/bip-0341.mediawiki
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.