Although the Magnacharger is a form of Positive Displacement Supercharger, the design is based around the Eaton Supercharger and is essentially an Air Transfer Device, not a compressor. Therefore it does not “condense” the air like one of the many Twin Screw units on the market. Compression takes place in the lower manifold of the Magnacharger kit, post supercharger, not within the confines of the Rotors themselves like it does with a Twin Screw. Since there is no compression taking place within the unit itself, there’s really no harm in running the Water/Methanol mixture through the inlet side.
That being said, although there won't be any resulting damage running the Water/Meth pre inlet (also pre supercharger), your gains won't be as dramatic as they would were you to run it on the discharge side, either pre or post intercooler brick.
The main purpose of the Water/Methanol mixture is to both lower ACT's by pulling heat out of the compressed air charge and increase octane rating of the fuel by combining it with the methyl alcohol in the mixture. From a cooling perspective, in order for the Water/Methanol to be most effective, the mist should be sprayed directly into the incoming path of the discharging side of the airflow where the compression (and as a result heating of the air charge) is taking place . If you introduce it on the inlet side, before the volume of air entering the supercharger is compressed post discharge, the misting effect is lost as is its value for cooling the charge.
You will still see some minor benefit though, due to it dropping some of the ACT accumulated during the heat soak of the supercharger case itself.....not to mention you’ll also still benefit from the increased octane (and therefore an ability to run more ignition timing) now present in the fuel....but it wouldn't be nearly as effective as it would were you to spray it post supercharger, into the heated air charge itself.
