I would really recommend you to remove the markers, I will agree with the rabbit (Kadeton) it is not normal - the game is supposed to eliminate all type of premeasuring as possible - so if you want a fair and fun game, where all types of strategies are fair balanced, I would recommend you to play without the deployment zone-markers. (btw. don't always trust your eye-measuring ).
I am not sure what "the Warmachine/Hordes ubiquitous linear obstacle" is, have not played it - however as long as both of you agrees on the Height-level of all terrain, the type of all terrain (sloped/edged/severe/normal/impassible), and use Malifaux walk/charge/jump/climb/fly/float abilities, you will do it right. Every measuring doing the game is top-down-view-angle so, as long as it is fair and same rules for both of you. I hope this helped! You might as well end up in some odd LOS-question, but that happens quite often (:
As far as I know, and I do play lovely Rasputina myself, her spell has a "gun-marker" which makes it a ranged spell, so ranged-rules applies, and next to that since "magical-damage" is not written on the spell-description, so I would not take it as "magical-damage". But I am actually getting a bit unsure. However if you play Rasputina, I would recommend you to play with snow storm who is also spirit, and then buff him with armor +2 - which actually makes him a good bodyguard. Also remember that Snow storm can fully heal (I did that against Lilith, she inflict only 3 wounds on my snow storm (she was btw. frozen to the obstacle/terrain), and then Snow storm clawed her to death, resolving in a 0-ability, eating her, and healing all his wounds. (a bit overpowered imo. but it works).