Just about 6 weeks ago I replaced my Lewmar #40 winches with chrome #40ST winches. I too was hoping the holes would match up. It seems like common sense to make them match but, sadly, they do not.
However the old holes are completely covered by the base of the new winch. You can easily find an orientation for the new winch where you can make new holes around the old ones. On my boat there was no reason to fill the old holes. The winches are in the cockpit, bolted to solid fiberglass with an opening under it for handle storage.
Changing the winches was about the easiest job I have ever done on my boat. That said, be careful when you take the old ones off. Don't grab them by the stem because you'll drop them over the side. Ask me how I know
Actually, I just lost one bearing.
I have no idea what the old ones are worth, but I am probably going to service them and keep them. I might put them back on the boat to use as cabin top spinnaker trim winches, because my existing spinnaker trim winches are well aft of the tiller end, which makes steering and trimming hard.
I paid about $700 per winch at Defender for mine, which was great at the time and probably still is. If you can get them for $500 each then its a steal.
All this said, you might consider Anderson winches instead. I believe they are made without plastic parts. And occasionally, very occasionally, my 10mm VPC sheets will slip in the clutch. On the plus side, the new winches are very easy to open for servicing and overall have been a great addition. My cockpit is small, so eliminating the need for a crew member to tail has been a big win.