Well, only talking about Yagyu Shinkage-ryu, Kamiizumi Ise-no-Kami and Yagyu Munetoshi were issuing licenses in the 1500s, before the bureaucracy really took off (not that there wasn't bureaucracy at that time). But given that "inka" was a common term for menkyo kaiden at that time, I suspect the real influence on menkyo and licenses was Buddhist practices, particularly Zen, of passing down knowledge and authority.
Josh Reyer
Swa sceal man don, žonne he ęt guše gengan ženceš longsumne lof, na ymb his lif cearaš. - The Beowulf Poet