[SFfiredog]

The staggered stack hights were definatelyto tune for the long/short intake runners of the standard BBC head. This was especially critical for individual runner intakes like the FI units shown. Many BBC single 4 and tunnel ram intakes of the day had the carb pads "twisted" in an attempt to equalize the runner lengths.
I read an interesting article in which one of the GM engineers that designed the BBC explained how the Z-11, or "mystery motor" of '63/'64 was built with equal length runners and 5 head bolts per cylinder.
To do this required more complex tooling/casting procedures and a higher rejection rate and IIRC different intake and exhaust rocker arms. The "bean counters" at GM nixed the plan and told them to design a head that cost less the produce and to use the same rocker arms on the intake and exhaust. They were able to keep the 5 head bolts but had to compromise the intake port design for cost sake.
BTW, The ZL-1 does have a head bolt that passes through the intake port. The hole is then plugged with an allen plug.
--Mike