Well, yes, sometimes the Year-End-Nº1 is a close battle between two (sometimes even three) players (for example, Courier-Edberg-Sampras in 1992, Sampras-Agassi in 1995, Sampras-Rios in 1998, Roddick-Federer-Ferrero in 2003, Federer-Nadal in 2009, Nadal-Djokovic in 2013...).
But close finishes also happen in GS tournaments. Nadal-Federer Wimbledon 2008 was almost a tie. Do you want to make them co-winners of 2008 Wimbledon? Do you want to make Nadal and Djokovic co-winners of 2012 Australian Open too?
One unique player has to be the one who wins a given GS tournament, and also one unique player has to be the one who amasses the most ranking points during any given year.
Another different thing is that you may not like the ranking-system for a given period. For example, many people don't like the ATP ranking prior to 1990, when it was an average of points obtained in sanctioned tournaments. But whether you like it or not, Connors was the one who obtained more points (under that averaged ranking system) in 1977 and 1978 (some people try to give those years to Vilas and Borg respectively saying that in a non-averaged ranking system they would have been above Connors; it may be true, but players competed under those rules then and I think it is unfair to change it retrospectively).
For example, if in 2020 they change again the ranking system (because it has been changed so many times, it could happen again) and under that new system some people evaluate past years and they find that, for example, in 2003 Ferrero would have been the nº1 under the new system. Do you think it would be fair to Roddick to "give" (retrospectively) that Year-End-Nº1 to Ferrero?.
Players (top-players) knew (in their time) what kind of results (during the last weeks of every year) they had to achieve to get their Year-End-Nº1 (under the ranking system they were playing), so it is unfair to take out or give Year-End-Nº1 based on ranking system of the future (or any period of time different than that of those players).
Anyway, I don't even try to compare players from different eras. For me the only sensible thing is comparing players from the same era and call some players "the best of their era".
But close finishes also happen in GS tournaments. Nadal-Federer Wimbledon 2008 was almost a tie. Do you want to make them co-winners of 2008 Wimbledon? Do you want to make Nadal and Djokovic co-winners of 2012 Australian Open too?
One unique player has to be the one who wins a given GS tournament, and also one unique player has to be the one who amasses the most ranking points during any given year.
Another different thing is that you may not like the ranking-system for a given period. For example, many people don't like the ATP ranking prior to 1990, when it was an average of points obtained in sanctioned tournaments. But whether you like it or not, Connors was the one who obtained more points (under that averaged ranking system) in 1977 and 1978 (some people try to give those years to Vilas and Borg respectively saying that in a non-averaged ranking system they would have been above Connors; it may be true, but players competed under those rules then and I think it is unfair to change it retrospectively).
For example, if in 2020 they change again the ranking system (because it has been changed so many times, it could happen again) and under that new system some people evaluate past years and they find that, for example, in 2003 Ferrero would have been the nº1 under the new system. Do you think it would be fair to Roddick to "give" (retrospectively) that Year-End-Nº1 to Ferrero?.
Players (top-players) knew (in their time) what kind of results (during the last weeks of every year) they had to achieve to get their Year-End-Nº1 (under the ranking system they were playing), so it is unfair to take out or give Year-End-Nº1 based on ranking system of the future (or any period of time different than that of those players).
Anyway, I don't even try to compare players from different eras. For me the only sensible thing is comparing players from the same era and call some players "the best of their era".