Hi Herman,
Re foot-marks in Kharosthi: long story and complicated: the place to start is pp. 21-28 of Andrew Glass's MA thesis (University of Washington, 2000) "A Preliminary Study of Kharoṣṭhī Manuscript Paleography”) which I think is available on line; and then his 2007 volume, Four Gāndhārī Saṃyuktāgama Sūtras: Senior Kharoṣṭhī Fragment 5 (Gandhāran Buddhist Texts, Volume 4. Seattle: University of Washington Press), pp. 88-91.
Basically, true footmarks are phonetically insignificant, incidental artifacts of the mechanics of handwriting (like serifs, Devanagari top-line, etc.). As Glass shows, they are very common and quite varied (as many as ten varieties) in manuscript Kharosthi. Such incidental marks are often (in various writing systems including Kharosthi) adopted into epigraphic writing.
This whole issue is however complicated because the footmarks can sometimes be hard to distinguish from, on the one hand, the anusvara sign, and on the other, the diacritical sign at the base of various consonants, which does indicate a variant (fricative?) pronunciation in intervocalic position; see Glass 2007: 107 ff., and related discussions in other volumes of the Gandhāran Buddhist Texts series).
Rich Salomon