1. We found that only a tiny fraction of users used the functionality of custom workspaces (especially multiple custom workspaces), and generally, the import/export functionality was a nice idea at the time but it was a bit of an overkill. In other words, while nice in principle, because it was never implemented really well, it would have been better if this functionality was never added.
2. In an ideal world, we should do something about this. In reality: because it's used by only a tiny fraction of users, we won't be able to fix this. We have a dozen or so "serious" or "severe" problems in both FontLab Studio 5.1.4 for Mac and 5.2.1 for Windows that we intend to fix. There will be one more final release of the FontLab Studio 5.x series for both Mac OS X and Windows in the coming months, which will contain some bugfixes and one important new feature. Due to our limited resources, the planned bugfixes only address these "severe" or "serious" issues. Unfortunately, the issue you report is not among them.
3. On the Mac, FontLab Studio 5.1.4 was pretty much a "mandatory" update to FontLab Studio 5.0.4 because the former was PowerPC and did not work at all on Mac OS X 10.7 and beyond. But on Windows, I see FontLab Studio 5.2.1 more of a "user choice" update. There are probably good reasons for which you may prefer to stick with 5.0.4, especially for all the design, metrics editing or scripting work. There are some changes in 5.2.1 towards 5.0.4 in these areas, which some people like but others don't.
4. The only area I recommend using FontLab Studio 5.2.1 rather than 5.0.4 is the actual font generation. Because 5.2 uses AFDKO 2.5 while 5.0.4 uses AFDKO 1.6, FLS 5.2 generates more modern and up-to-date fonts (although, in fact, TransType 4 is even more modern and is possibly an even better tool to generate TTFs and OTFs out of VFBs).
5. You can have both FontLab Studio 5.0.4 and 5.2.1 installed on the same machine, and use each of them whenever necessary. I agree that this is far from ideal, but may be the scenario best suited for your needs.