I just measured a couple of things I had here, to make an educated guess at it: the Honda head gasket(s) I have here (used) are thicker than the Athena, Vesrah, and the unlabelled ones I've recently received with some 836 piston kits. The plot thickens...
Here's what I surmise, as I never had any interference issues when I used only Honda's parts: the new aftermarket gaskets don't "understand" that there were various different engine designs. I have seen this with aftermarket parts for my Fords before, too. The Honda gasket I just measured, fully collapsed after 25k+ miles on its engine, is 1.20mm thick. This means it cleared those dowels, compressing only their rubber collar seals, when the head was torqued down. I don't have that head handy: it is running around town on a cafe' bike I just finished last Fall. If I did have it, I suspect there would be no dowel marks on the head.
The (new) Athena gasket I have is 1.15mm thick at the same place, and the (new) Vesrah is 1.8mm thick. I think the Vesrah would work OK in this scenario.
Here's what I would do, if I were assembling that combination (and I might be, soon, on a build I'm gathering together now):
1. Measure the thickness of the new head gasket.
2. Set the head and cylinders together (as you already have), measure the open distance.
3. The head gasket will not compress more than 25% of its thickness, typically. So, I would shorten the dowels by 10% more than the projected thickness of the assembled head gasket. This should leave the dowels captured in place to support the rubber seals without hitting the head and stopping the closure.
One of the things we must deal with these days are all of these (young) vendors who are jumping into the burgeoning vintage markets without benefit of original knowledge. In particular, I have noticed that in the area of gaskets and seals, there are some uneducated products appearing to make our work a little more challenging (but still completely do-able). The gaskets in the new "red" packaged kits we are seeing from Japan have thicknesses that correspond to modern bikes' parts, which are far more accurately machined than 1960s parts, and which use thinner gaskets. Some seals we are seeing are actually built backward (tach drive seals on the CB750 come to mind), so they need close inspection before installation.
The old gaskets (and Honda's own, today) come with a paraffin-like sealant embedded in the material, and are nearly twice as thick (about 1.7 times, actually) as the afore-mentioned "unnamed" Japanese gaskets I have here. The new ones do not, so I think they will need Hondabond or the like on them at assembly. This is not usually done for head gaskets, though: they should have a sealant on areas around the oil ports already. If they don't, use Felcobond (from Fel-Pro) thinly on those areas to prevent oil leaks around the passages: this stuff is similar to the stuff normally painted on the Honda gaskets.
In this particular area, there were 4 dowel length used on the heads and cylinders over the years. The longest ones were 22mm (I think), while the shortest ones were 12mm, and the "others" are 18mm long. The parts fiche I've been looking at don't have it right, either. The K0-K1 engines had one "set" of dowels, the K2 (after about 11/71 production) through early K4 had another "set", and interspersed with the early K4, through the K6, a third "set" appeared with 3 different lengths. The "F" engines all shared a common 2 types, too, but it seemed they differed because the F0 used 4 (short) and 8 (long) of the different types, while the later ones used just 4 and 4 of each, but added O-rings in other places and little recesses in the head (the F2/F3 engines) to help reduce hot oil leaks.
In the end, almost all of the heads and cylinders (after K1) will interchange with a bit of puzzling through the lengths of the dowels (or lack thereof) and the thicknesses of the O-rings needed (although some combinations may not be the best idea, like mixing "F" and early "K"). Let your calipers guide you: I recently discovered, for instance, that the O-rings Honda now sells for the head/cylinder interface for the K1 engines are not the same thickness as their present head gaskets require: they are too thin at 1.8mm. A standard 2.0mm thickness fits the Honda head gasket thickness, letting the O-ring compress about 20% during the torquing (the former is about 6%). If you had used the thinner Athena gasket, the same 2.0mm O-ring would be too thick: those gaskets will require about 1.5mm of cross-section thickness to prevent over-squishing, splitting after a couple of years and causing a leak.
So, measure the gaps, measure the head gasket you will use, and use the rule of 8% to 18% of "squish" for non-pressurized O-ring seals, and 12% to 22% for pressurized O-rings (under the cam rocker towers, too) and you'll be rewarded with a dry engine for a lot longer.