But also there are issues in that by separating the competition into two stages you split the league - because by default the entire league isn't playing for top 4 positions - into two separate groups. I don't happen to think that's healthy.
I don't see that that necessarily follows.
Firstly, it's hard to think of a sport in which every team enters the season aiming for the same goal. Different teams will always have different playing and financial resources, and therefore different goals. For every team to begin the year with a realistic chance of winning the league, you need no relegation (so effectively a franchise system) and some means of evening up playing resources (like gridiron does with the draft).
In fact the AP, for all its distortions, is one of the best leagues for competitiveness anywhere. It doesn't have the huge resourcing distortions of the roundball premiership, the Magners or the Top 14. At the outset of the season, 10 of the 12 teams would have had hopes of a Top 4 finish - which is more than in most professional leagues.
Secondly, prioritisation of certain games happens all the time in professional sport. Tennis players and golfers pick and choose their tournaments. Football teams and Rabo teams prioritise some competitions over others. It's even been shown to happen in sumo (pace Freakonomics).
I'm pretty sure that Quins change their training regime to prioritise player welfare over winning during January and February. Rugby's an attritional game and is played in many different conditions. Nothing wrong with managing your performance to optimise the number of good performances over the course of a long season - and this would happen with or without the playoffs. The playoffs just give a team a different problem - in a first past the post league, you can gamble on building an early lead and then hanging on; with playoffs you have to ensure you've got a decent squad available for the endgame. Both routes will need coaches to prioritise. The playoff one probably has some benefit for player welfare in the long run, though.
Thirdly, until a couple of games ago, all but 3 teams were in the hunt for Top 4 or at least Top 6 places. Even now, only Bath and Worcester are going into the final three games with little to play for. When every result matters to 10 of your teams in the run in, it makes for an exciting sport. And this happens every year. For rugby to be viable as a professional sport in a football-dominated country, it helps for it to have a structure where as much as possible goes down to the wire.
In a first past the post league, it could well be over a month earlier - less interesting for the fans.