[Miscellaneous Android Development] Almighty2:
I think the thing is Google Play Store keeps changing the place where the version number is listed. Atleast it's better than the ones that says varies with device under the version number. The Update button worked fine for me in BlueStacks, maybe it's because they are doing it by region for all we know.

SuperSU is the only one that has a Professional version where you have to pay for it as well. I'm sure koush when he made Superuser borrowed features from others as well. I know in CM 10.3, there are some things that are broken with koush's Superuser that SuperSU fixed. Actually, it's not a mess updating it, the mess came out because of Android 4.3+ as all Superuser/SuperSU had problems and they tried to fix it so it would work correctly in 4.3+ and ofcourse when it did, it also broke stuff with earlier Android versions.

When you did the Root.fs for BlueStacks 0.8.1.3051, you packaged it with koush's Superuser 1.0.2.1 which worked fine but any version newer than that such as 1.0.2.3 and even the one on Google Play Store now, the apk installs and it installs the su binary but it's broken as root programs that need permission are not getting the prompt to ask for permission and when you run su in the terminal on any Suepruser version newer than 1.0.2.1, it will just take some time and then time out and return with "permission denied" so in the case of that, the su binary is not able to talk to the apk. So no one said Koush's Superuser didn't update except programs that need root aren't able to get prompted to grant/deny access. The fix to that was in Google Play Store to uninstall updates for koush's Superuser and then run the Superuser app which is in /system/app and basically Superuser 1.0.2.1 again, it will prompt, download and install the Superuser 1.0.2.1 su binary on it's own. So the issue with SuperSU is different, it has a working su binary but so far, seems like the only way to get the su binary working is integrating it into Root.fs as other methods for whatever reason, the apk is not recognizing it as the correct binary.

Last Root.fs works fine as SuperSU v1.69 prompts and gets granted permissions and Google Play Store on Blue Stacks does have auto update turned on by default and everytime Play Store updates itself, it seems to return to the auto aupdate setting so it would still update to the latest version since Google Play Store only updates the apk, updating the su binary like any SuperSU/Superuser would require the user to actually run SuperSU/Superuser and it will prompt to install the su binary as from what I read, it's the su binary that determines which apk provides SuperSU/Superuser to the system as you can have all the different SuperSU/Superuser installed but whoever's su binary is used is the one that basically has root control.

Kind of weird since as long as you replace the initrd.img and Root.fs with the files provided, you should have SuperSU v1.69 with the working su binary as I mentioned, a few days ago, I tried updating to SuperSU v1.75 and ofcourse it broke and the newest koush Superuser from Google Play Store didn't work either as the su binary was not talking to the apk and uninstalling Superuser and the updates for SuperSU didn't work either as it's supposed to go back to the 1.69 of SuperSU as the apk is in /system/app but in App tray, SuperSU was grayed out. The fix was easy as all I had to do was kill BlueStacks and then replace the Root.fs file and it's back to SuperSU v1.69 with a working su binary. Did you remember to kill BlueStacks before you replaced the files?