Keith,
Short answer for me is .016" usually means .016." I hadn't thought too much about if you changed rocker ratios, so here's where the long answer may change. Most of my advice comes from dyno work I've done with Dave Anton at APT on A-series and B-series engines. Dave taught me to try opening them up a bit more than the cam manufacturer recommended if it's a higher ratio rocker than stock. So he may have added .02-.04" clearance if the ratio is higher. What we'd do (and I still do) is try it on the dyno and get the best numbers we could. Generally, the additional clearance got us some low-end without sacrificing top-end and improved idle quality as I mentioned before.
I haven't thought about it anymore than that until you posed this question, but maybe the long answer is that .016" means .016x(% increase of new rocker ratio)? That sounds smarter than my guess-then-dyno (aka trial and error) system anyway.
Carl