The skin-based transducer used to measure the concentration of CO2 in the skin must generate some chemical response that may be interpreted to form a valid approximation of the blood proximal CO2 concentration. This work introduces the Kernel-Gated Acid-Base Fusion (KG-ABF) carbonate gate for the paired microneedle pH and carbonate data. The key challenge is how the combination of the carbonate filter with the time-weighted animal level fusion impacts the discrepancy between the estimates based on the intradermal readings and the terminal blood-gas PCO2 levels compared with the unfiltered averaged or last microneedle measurement only approach. The analysis dataset consists of six conditioning conditions of the rat skin and twelve animal times from five anesthetized rats. The KG-ABF algorithm assumes the two measurements as a coupled acid-base signal, withholds the blood-proximal CO2 estimation if the measurements of the carbonate, bicarbonate, and transformed PCO2 values are less than useful chemically, and applies weights to the accepted intradermal CO2 values as a function of proximity to the terminal blood sampling. In the full set of ex vivo samples, the intradermal and reference measurements differ by 0.9 ± 0.5 % for pH, 14.2 ± 2.8 % for carbonate, and 10.3 ± 9.7 % for dissolved carbon dioxide. The in vivo gate filtered out one rat 4 sample and accepted eleven animal time measurements from rats 1, 2, 3, and 5. The values for accepted KG-ABF values were 14.7, 53.0, 51.2, and 27.2 mmHg and the reference readings correspondingly equal to 18.8, 48.8, 53.7, and 25.4 mmHg. The achieved mean absolute error amounts to 3.1 mmHg, the root mean squared error equals 3.3 mmHg, and the maximum absolute error is 4.2 mmHg. These results support carbonate-gated interpretation as an essential analytical layer for intradermal gas-sensing patches.