This is an interesting discussion.  Like many other members on this forum, I fall into both the nostalgic player + the semi-nutty collector categories.  If you look at PC Genjin 3, even in Japan now the local store prices are not that cheap.  Do a quick look on Yahoo JP auction, and you'll also see the game is not that easy to find.  Combine the fact it is actually a pretty entertaining game (in my opinion better than Bonk 1 or Bonk 2), if you can grab it for $30, by all means get it.  You have nothing to lose except $30 greenbacks, which is worth less and less by the day as JP Yen is now kicking our ass at 87 yen to $1 USD!  (when I worked in Tokyo back in 2006, and getting paid in yen, it was costing me freakin 120 yen to get $1 USD!  I shoulda bought more PCE games back then.. . 

)  
My general rule of thumb is to get the best version of the games I want to play/collect... and if there are huge price differences but little to no gameplay variations (i.e. Bonk 3 US v.s. PC Genjin 3), than getting the latter is a no brainer.
Magical Chase PCE version is very rare by itself, with or without the US effect... so I can't really draw parallels to that.  
Flip-flopped, SplatterHouse PCE version is clearly much more desirable/harder to get these days compared to the TG version.  That's what makes life fun... we have choices...  now I need to go on debating whether or not to drop $2000 for US version of Magical Chase or be happy with my hard-to-find PCE Fan version of th ePCE Magical Chase.. (just kidding, I'm perfectly content.. haha)