If you properly use any number of decent protractors, you should be able to attain proper alignment. When you say "multiple geometries," are you really talking about different null points (Baerwald, Lofgren, Stevenson)?
I use to have a Helikon (I now have a Titan). Lyra cartridges have a very narrow specified tracking force range. It is best to stay within that range. Not only does this prevent any damage, but, the cartridge's suspension is set up to ideally work with that particular loading and the coil and former will be in proper alignment with the fixed magnets with that loading. There are those that advocate higher tracking forces than the manufacturer's specifications; I personally would not stray outside of the recommended range even if the sound were better.
I found that both the Helikon and the Titan are a bit sensitive when it comes to VTA--even small changes are audible. But, that appears to be the case with most cartridges that use narrow profile "line contact" stylus types (e.g., Shibata, Ogura, Ortofon Replicant).