I've worked at a Montana equiped shop for almost a decade, though now I moonlight as I have moved on to more exciting things. We had a "smearing machine," and have also used repair candles. We use a Montana Crystal glide machine (originally a single ski model, and now a pair of ski/snowboard model, newer than the one pictured there).
With regards to smearing vs candling, the smearing machine we used strictly clear P-Tex, as it was invisible no matter the colour of the base. It was better than candling in my opinion, because so long as the operator knew what they were doing in regards to clearing the feed plate and controlling the pass speed, you would get no burning of the P-Tex (causing the brown). When using candles, Black is easier because though it may char, it doesn't show. Working with clear candles and keeping the repair free of char IS possible, but just requires a great deal of care.
Machine vs candling in general; I would stick with teh machine, partly because it speeds up the process, and as I say, a competent person running it will get better results when compared to candling - but they have to be knowledgeable and experienced.
There is no difference between black and clear in terms of the ability of the repair to take on the base structure from the grinding machine.
The bottom line is that the tech couldn't be bothered.
There is a fix available to you, but basically, you'd need to cut the old fill out and have them do it right. Given their inability to do it right the first time, I'd be tentative to ask them to do that. If you want to do it yourself, you should see if they will do a fresh base grind for free when you're done with the P-Tex. For a colour difference, as bad as it is, I wouldn't worry about it. Keep an eye though, because if they haven't prepped the gouges properly, the fillings may not stay in.
As for the Montana, they are good machines, and while a bit of skill helps get better results, it's pretty tough to screw up a basic tune. Not impossible, but tough.
Hope that helps.