I did some heavy stochiometric analysis of the KrZ synth and of the second one which you refer to from the rhodium archive:
First there is an error in the noting of how many moles of tryptamine HCl - it should be 51.02mmol, 62.4mmol at 10g is precisely what tryptamine freebase would be.
And yes, you are right, the NaCNBH3 should definitely be added to the mix last, because it will react with the water in the formaldehyde, the formaldehyde, and it will deaminate and/or quaternise the tryptamine.
Personally I don't think much of this reaction because of the very high quantity of water that is introduced into the mix via the formaldehyde solution.
As to the time factor, if you are looking at a proper scientific description of a reaction which says 3 hours, it's probably true. The cooling is likewise unneccessary (though probably decreases the reaction of the NaCNBH3 with the water and tryptamine while they are being mixed). Change the order and it becomes irrelevant. Likewise with the non-reactive atmosphere - possibly it might decrease the risk of hydrogen sparking, which would be released by the NaCNBH3 as it reacts with the water.
And finally, there is a bit of danger in this reaction that KrZ describes - though unlikely, there is (according to what is written in that second process) HCl ions floating around, and according to hazdat sheets about NaCNBH3, acids liberate the HCN - well, obviously it can't be weak acids they are referring to, rather it must be strong acids, and HCl ions might get a bit messy if they unhook. Though they wouldn't do that an awful lot, it is something to be aware of. Use freebase and you avoid that problem.
A side note, the first one has incorrect quantities of formaldehyde (30 instead of 45g) and incorrect quantities of NaCNBH3 (50 instead of 125g) I think the amounts of acetic acid are wrong too, but I don't know exactly what molar ratio of acetic acid is required to protect the tryptamine. In the second one it is almost 4x molar to the tryptamine, or 2x molar to the formaldehyde, so I would say that you actually need 60g in the first rxn.
This reaction would be much better if you could have the formaldehyde dissolved in anhydrous methanol rather than water. Perhaps the two could be mixed and the water salted out?
C12H16N2