Just to let you know that you have done everything properly. You should have excluded carpet as it is a surface not played by some players you wish to compare. By allocating the same weight to each surface and doing averages of averages you have addressed the issue of surface bias arising from different number of matches played on each surfaces.
But there is a problem. I think you are a fan of Djokovic. Do I have that right? The inconvenient truth is that HCs are the most important events re careers today because not only are more M1000s played on that surface, two of the 4 majors are there also. And the WTF. So today, from a practical perspective, it makes sense to be strongest on HCs. When two of the four majors are on that surface, it makes sense to put top priority on dominating on that surface. Is this what you are calling a surface bias? Or is it about the bragging rights of winning Wimbledon?
Looking at thing practically, today you want to be best on HCs, then second best on clay IF you are looking at career records for winning all events and especially for that in combination with majors. That would logically give Djokovic and advantage in that HCs are his best surface, and more matches are played on HCs by far.
If you are a traditionalist and give the greatest weight to Wimbledon (which I do not), then you will see the whole matter differently.
But if you take a straight career average of match wins, or big event wins, you are merely reflecting the reality of the tour. I see 215 grass matches for Fed and an 87.13 record, and my count includes the Olympics and DC. To me it seems pretty obvious that if there were a whole lot more grass events, Fed would have a higher W/L%. And if the majority of matches were on clay, who knows how high Nadal would be.
This doesn't matter, but "it is what it is". We have to deal with the tour as it is, which means counting all matches, including carpet, and even wood in other eras. Then we have an even playing field, simply comparing careers as they were/are. Today including or excluding carpet will have a negligible effect on the results because it is such a small factor.
Taking an average of the surfaces ignores the reality of the balance of these surfaces regarding frequency of which each surface is used for events.