Older Sugino cranks use the ISO standard and I run into them fairly often... replacing these with JIS spindles has not caused problems although you do have to adjust for the variance in chain line and use a narrower spindle when you use an ISO crank on a JIS spindle or new cartridge bb to get a proper chainline.
Conversely, with a JIS crank on an ISO spindle you need a longer spindle but with these I usually replace the bb as I do not have a huge stock of ISO spindles and JIS spindles and bb's are plentiful. This is also better for the JIS crank as using the longer spindle can cause increased wear at the interface.
And then you get those odd cranks like Gipiemme 100 which use the same standard as Ofmega and Avocet and require matching spindles... I have a beautiful model 100 here that just needs a proper spindle so I can install it or will have to pass it along to someone who is looking for one of these.
In practice this has not caused any issues over many thousands and thousands of miles and is not really something that modern mechanics have to deal with very often and it usually baffles them.
I am really pleased with my old Sugino Maxy with it's odd 171 mm arms... it has been rock solid (later model) and who doesn't like drillium ?