The short version of my issue at hand,
You can enable the Android SDK installer to run on Windows x64 with JDK x64 installed, by exporting HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft\Java Development Kit registry key, adding Wow6432Node to all registry keys in the exported file and reimporting it back (should show in regedit as HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\JavaSoft\Java Development Kit as well).
Note I have both x64 and x86 JRE installed. If you have only x64 JRE, you might have to export the whole HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft registry key and reimport it under Wow6432Node. Although, I believe that the Android SDK installer just checks the JDK registry key.