Question: Can the Inlier limit and Hotelling’s T2 limit be interpreted as confidence intervals?
Answer: For the Hotelling’s limit your interpretation is correct, and you can set the desired significance level. The inlier limit is not associated with any probability limit. Rather, the pairwise Mahalanobis distance is calculated for all points in the calibration set. The minimum distance to a neighbouring point then is found for all observations. The maximum of these ‘shortest distances’ gives the inlier limit. If a new observation exceeds the inlier limit, this means that this point is farther away from any calibration point than the shortest distance between calibration points.