To my knowledge, it should be possible to configure warptorio in such a way that you can make effective use of the platform stairs and the techs/upgrades without being subject to warping and whatnot.
Please keep in mind, Warptorio is not designed to be added to an existing save or scenario in any way, shape, or form, instead it is only intended that Warptorio is used when starting a new save, only, with the only exception that the save started with warptorio in the first place.
I would suspect that's why you had surface conflicts.
I welcome you to tinker with the scripts, however I ask that if you choose to distribute your changes that you clearly describe your changes and the fact that there is no warranty offered with regard to the situation that anyone's save files can become corrupt and I cannot fix them. If you can offer that guarantee to fix their save files yourself in the event of major catastrophe, by all means, but I cannot offer that guarantee on unknowable changes made by others like yourself.
In short, it is intended you are able to adjust difficulty settings of the base warptorio2 mod to achieve this, if I have missed any particular settings please let me know them.