In SSI Web, it's possible to insert questions anywhere during the ACA questionnaire. So, it would be possible to insert a holdout pairwise ACA conjoint question within the ACA Pairs section (formatted just like ACA Pairs). You'd use the Free Format question type within SSI Web to script that up (borrowing the HTML from another ACA Pairs question (with some additional tweaks needed).
Or, you could add holdout CBC-looking choice tasks after ACA questions, using Free Format questions (or CBC Fixed Tasks, by inserting a CBC exercise after the ACA exercise).
Also, if you are using ACA/HB software to compute ACA utilities, you can set it into the mode of only using the ACA Pairs information to compute utilities. This will give you an R-Squared for each individual that is based on the internal fit of the utilities to each individual's ACA Pairs questions. But, why not also leverage the Priors ratings in ACA/HB as constraints...and ACA/HB will give you an R-squared that incorporates the consistency of responses across ACA Priors and Pairs questions, giving you an even more complete view of respondent internal consistency.
The standard "R-Squared" that ACA uses to compute the consistency between the early parts of the ACA survey (Priors + Pairs) vs. the Calibration Concepts (purchase intent questions) I don't place as much confidence in. It's quite possible that folks just don't understand the Calibration Concepts questions very well, so that can foul up the R-Squared measures, even though a person was quite consistent in the early aspects ot the ACA questionnaire.
Just some ideas to chew on.