Personally, I wire the winch independently of the truck to the battery (through a disconnect). One solid ground, one solid hot, no interruptions. I am also not a fan of running high amp alternators through the starter(hot). It is a "short cut" but every time you introduce an electrical connection/splice, you have voltage drop, heat, and a potential of corrosion/fault (whether through the connector on the cable or the union). Checking the resistance of the system is not accurate--because under high amperage loads, you can have a poor connection of trying to transfer massive amperage where in a resistance test from a standard meter, you could technically have just one strand of wire making the connection and have ~0 resistance when in reality it is incapable of transferring full amperage.
As to disconnecting the alternator, no engine running, and running the winch--there would be nothing to kill the alternator as the full load goes through the battery. I have done this for over a decade when bumping stuff around the house (not recovering a truck) when I need short bursts. I do have a massive battery, too (Oddesey 2150). However you should never disconnect the battery to check the alternator while truck is running and there are many reasons for this including that the charging system actually outputs AC voltage (that is what the zeneer diodes and the rectifying circuit is for--to convert to "approximate" DC and that is why the battery, acting as the full DC buffer in the system, is important as well as providing a more concrete DC ground to the system.
I am going to concede that there two methods, both good, for hooking up disconnects but only because I am tired or arguing over it. They both work and depending on the many factors, both are completely applicable between switching ground or switching hot...(sort of). For me, I switch hot--and I do that intentionally and after much thought. My logic is simple--First, I don't like having a hot constantly run to the winch. If I switch the hot, the winch is not hot nor is the cable running to the winch. If I switch ground (and the truck is running or "hot"), then the cable is hot, the winch is hot, (even with the winch ground is disconnected) and if I bump the winch, it will ground the winch through the housing. THIS HAPPENS and I had my winch case glow red hot before I realized I had the ground disconnected and it could have destroyed the windings. If you are in an accident and your cable is hot or is worn, you can still create a direct short as your truck is still grounded (and it has to be in order to still be running). In the "switch the ground" scenario, that means you can NOT use the truck at all if the disconnect is disconnected. I have a two pole switch but this applies if you have a winch discconect AND a truck disconnect too. I use my winch 1% of the time---so it should have it's own disconnect.
Those that say "switch the ground" has to always switch off the entire truck all the time. Either EVERYTHING is disconnected or EVERYTHING is on. If they "attempted" an in-between solution where the truck is grounded but other things are disconnected, then I feel that they have not learned the lesson yet that there are multiple unseen paths to ground in a car (through stereo, alternator, starter... so many!) but they will eventually. It is not a good way to switch a winch. NOTE: I do switch grounds for a lot of my electronics-- but they are run through fuses and are not capable of pulling hundreds of amps...
