In individual stroke play, for example, the 95% Playing handicap Allowance is because higher handicappers would "benefit" over lower handicappers if they could play off 100% of the course handicap (which has been discussed on numerous threads). Therefore, the higher handicapper gets a bigger reduction towards zero than a medium handicapper (effectively, if handicaps were to decimal points, the difference in handicaps between golfers would no longer be 100% of course handicap, it would be 95% of course handicap between all players). I used 50% in my example simply to make it much clearer.
Why would you change the rules after crossing the arbitrary threshold of zero?
Again, let us use the 50% example. A 6 course handicapper now only gets 3 shots compared to a scratch player (as the scratch player is still off scratch). So, the handicap allowance is there to say that, although there is a 6 shot difference in course handicaps, it is only fair in the competition to give the 6 handicapper another 3 shots compared to the scratch player. So, if you compared a +6 handicapper with a scratch golfer, then it would also be true that the scratch player should only get 3 more shots than the +6 player, not 6. Hence the +6 golfer becomes +3.
The issue you are having is that you are simply focusing on zero and upwards, and see that in absolute terms, players get less shots than their course handicap when applying these allowances (unless they are off scratch). You are then logically assuming that the purpose of these allowances are to give people less shots, and then this falls over when you look at plus players. HOWEVER, allowances are NOT to there to give players less shots. They are there to provide a fairer relative difference between all golfers based on the format.
Forget actual Zero for now. Imagine absolute "zero" was +6 (the lowest a handicap could go), and allowances were based on the difference between this absolute zero value.
So, using 50% allowances again and using the same course handicaps in my previous post
Player A Course Handicap = -6. Diff from -6 = 0. Playing Handicap = -6 - 0x50% = -6
Player B Course Handicap = 0. Diff from -6 = 6. Playing Handicap = 0 - 6x50% = -3
Player C Course Handicap = 20. Diff from -6 = 26. Playing Handicap = 20 - 26x50% = 7
So, each player gets 3 shots less (in absolute terms) than they did previously. But, the relative difference between them remains the same. That is key. If you applied a different rule for plus players, then you would no longer have equity