You need to use the appropriate class and calculation. Unqualified default calculations are probably using the RMS nominal-maximum voltage, in the presence of transients such as mains voltage of given category, and, yeah, those dimensions can get quite large. Since that would be a breakdown of easily, say, 10kV -- plus contamination factor.
For functional purposes, transient limited (peak voltage as given), not much clearance is needed, and in particular, the voltage between any given pair of conductors is all that matters. In a PMT divider chain with say 100V per dynode, you can use just a little bit (0.3mm or so) and it's fine. As long as the spacing along the chain to surroundings is adequate, which will probably grow along the chain (depending on what ground is relative to; usually the top dynode). And that will need to be several mm.
Tim