BIP-69 specifies the lexicographical ordering of inputs and outputs. This makes it harder to fingerprint certain wallets and increases privacy. The metric reports transactions being BIP-69 compliant, but this does not mean that the inputs and outputs are purposefully ordered to be BIP-69 compliant. Transactions with only a few inputs and outputs, for example transactions with one input and two outputs, are common. But these transactions have a high probability of being BIP-69 compliant when the inputs and outputs are ordered randomly. All transactions with one input and one output are automatically considered to be BIP-69 compliant. The percentage reported here can be considered as an upper bound.
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