I found a correct registry and I fixed all but one problem. Individual 32 or 64 bit installers now install shortcuts correctly and show in installer the correct Program Files folder.
But when I have a mixed 32/64 bit application, which includes both 32 and 64 exes, the installer always points to Program Files (x86), which is a problem because even if I correct it manually, it will install the 32 bit part of the application, not the 64 bit which I need. Seems that windows can't see 64 application in mixed installers at all.
I tested with 3 mixed installers, FoxitReader832, ashampoo_winoptimizer_15_15.00.05_sm and Total Security 360TS_Setup_9.2.0.1164