Product line decisions are made YEARS in advance. By 1991, Porsche new that the door was closing on the 968 and 928 leaving Porsche with just a 911.
Also, in 1991-1993 were severely POOR economic years. Global recessions, high build costs, labor etc were killing porsche. Thoughts of Merecedes or VW buying Porsche were a very real possiblity.
The only way to expand their model line ups was to make parts common to both. To the detriment of 911 fans, this meant that the 911 (996) and Boxster (986) were to look alike. Even more detrimental to 996 fans, was that the 986 came out first. The sucess of Porsche's 993 (911) allowed them the luxury to NOT rush the 996 to market. Ideally both cars would have come out at the same time, not a couple years apart.
The Boxster was has widly succeeded in expanding Porsche's model line up (not many manufacturers can be sucessful with only one product) and their bottom line.
As for the other, original questions,
1) Economy of scale is part of it. That's why they got rid of the 3.2 in the 987S. Simplify product line up. One base motor.
I would also wager that the "next" base boxster will enjoy another diplacement boost, perhaps to a 3.0L as you mention.
The original 986 had a 2.5l with 201hp. Then a 2.7 with 217.. then with 228, and in the 987 with 240 and now 245, 10 years later, the base motor has nearly 45 more hp. Thats a nice way of improving the breed without completely outdating the previous version. Heck, the next base Boxster might have a 3.0l with 260hp... you never know
2) I don't think Porsche is conservative with redlines. My 3.0L 911 redline was 6250. My 2.7 Boxster redline is 7200. 7200 is a pretty high rev limit in my opinion.
3) The GT3 motor is NOT the same motor as the regular 996/997. It uses the same architecture as the GT2 (turbo) and regular Twin Turbo. This motor harkens back to the GT1 motor of the late 1990s.