Get both, sell the one you don't want here. To me. For a greatly reduced price. Problem solved.
+1 ^
Hmm, I hate to say it, but this is the best advice on this thread.
However, if you only want to buy one keyboard, I say get a RealForce 87U slient version. Here's why:
1. Topre v. HHKB Pro 2: Topre is better for you than HHKB Pro 2, because the layout is going to be more familiar, and therefore easier to use from the start. HHKB Pro 2 requires a learning curve. However, once you master the alternative layout of the HHKB Pro 2, of course, typing on your HHKB Pro 2 will be just as fast and easy as on any other keyboard. But you will need to invest the time. Do you want to do that on a $450+ keyboard? IMHO, due to the non-traditional layout, the HHKB Pro 2 is a secondary keyboard, and is definitely not a primary keyboard for daily use.
2. Bubble Keys: The bubble 1x Windows keys are part of the appeal of the Topre keyboard. I don't see how it's a negative. When you see those bubbles, you know it's a Topre. It's like saying you don't want to see a blue and white Bavarian flag logo on your BMW.
3. Variable v. Uniform weight: Something you may not have considered is variable weighting of the keys. Variable weighting is better for typing, while uniform weighting is better for gaming, if you use the WASD cluster for gaming. So, I would say that if you are doing more typing than gaming get the variable. If more gaming than typing get the uniform weighted keys. From your post, I gathered that you are a student. As such, you should be spending more time typing than gaming, anyway, so get the variable.
4. Silent v. Standard: The silent version is superior to the standard version. The "thock" of the silent version is far more appealing than the "thock-clack" sound of the standard versions. Is it worth $100-$150 more? That is a personal preference, and I can't tell you how to spend your money. However, I can tell you definitely that the silent version sounds better, is more appealing, and feels more luxurious. I highly recommend the silent, but I honestly cannot tell you it's worth the premium price, so you have to decide this one for yourself. One other caveat is that the silent version only comes with variable weighting. I have never seen a uniform 45g silent version of a Topre keyboard. Also something to note, the standard Topre switch is black, while the silent version is purple.
5. Price: Let's be honest about this, you are venturing into the very top-end of a luxury market, when you are choosing between Topre v. HHKB Pro keyboards. Either way you are going to be spending a a lot of money for a keyboard. Nobody needs to spend so much on a keyboard, since there are so many cheaper alternative ways to get a high-quality mechanical keyboard. However, since you are seeking the top-end, you might as well do it right. IMHO, the top-end is not a place to start bargain hunting: you won't be satisfied if you try to save a few bucks.
6. Conclusion: So, what is the take-away message here? Get the RealForce 87U silent version, and get one with white keycaps. It will cost you some serious greenbacks, so I'm not trying to save you any money. But I am trying to give you some good advice on how to enjoy the significant amount of time you are going to spend typing away at your computer. And really, what is more important than that?