But, to answer your actual question, a bare wire isn’t, in itself, problematic so long as it doesn’t short to ground (the engine case) or another coil. I don’t know how conductive engine oil is, so it might be worth sticking a blob of oil-resistant (which seems to also be bathroom-type) silicon on there just to be sure but I’ve never known anyone bother. Presumably it’s non-conductive.
Are you looking for a problem you know is there (“One coil shorts to ground and I want to find out where”) or using your normal speculative process (“something went wrong so I’ve removed a component at near-random and I’m hoping to blame it”)? You can measure for a coil shorting to ground quite easily, but only when the whole lot is assembled.
But, in case you’ve forgotten, I’ll explain the measurements to take. Ressemble the engine and then start by drawing a diagram:
But, instead of “3-4” at the bottom of the table on the left write “3-1” 
That rectangle near the top is a representation of the plug on the end of the lead that goes from the stator to the rectifier (the engine end of the connector, not the rectifier end). We’ve numbered the coils fairly arbitrarily so that we’ll know where any problem we find is.
Firstly, fill in the “Cool Rgnd” figure for each pin, that is the resistance between that pin and the battery negative terminal.
Next start the engine and, before it warms up, fill in the ‘cool’ half of the Vac bit of the table at the bottom. These measurements are the AC voltage between each pair of the pins in the connector and you’d expect something around 20-50V in my limited experience, but start with the multimeter set high and come down until it gets accurate. You want one measurement at idle and another at whatever speed the manual suggests to use when you measure the voltage across the battery terminals to check that the battery is charging.
Wait for the engine to warm up, and then take all the same measurements again and fill in the ‘warm’ half of the table. Also, measure the resistance between each contact pair here and fill in the column to the far right.
Stop the engine and, while it is warm, fill in all the “Warm Rgnd” numbers by repeating the measurements you started with.
You should have 21 numbers.
Now:
- Measure the resistance between the battery negative terminal and a bit of unpainted engine case (the threads on one of the spark plug holes is a good place to try)
- for a three-contact reg/rec measure the resistance between the lead that plugs into each of the two grounds and the battery terminal. For a two-contact one measure the resistance between the single ground and the battery terminal
- Follow the haynes manual test for the rectifier.
+10
