It's worth noting that the MUTCD language in § 2E.14 does not actually mandate the use of uniform criteria for space padding, so Caltrans can claim it is complying on the basis that it is choosing truss depth (and thus the height of all signs on the structure) according to the height of the tallest legend block on the signs.
Plus, as has been noted, other state DOTs have their own ways of fudging the criteria. For example, we're all used to three-quarters capital letter height for interline space padding, but Minnesota DOT allows this to vary from half to full capital letter height.