“It costs what it costs.” Sounds elitist to say that, but it’s true. Different tailors/alterationists in different cities and locations will charge different prices. My tailor in the downtown Chicago Loop charges higher prices because of costs associated with doing business at that location than a tailor might charge in the suburbs. Put This On has a price-range list of how much suit alterations cost.
Typically, I tell people to set aside $100-150 for alterations and always factor that into their purchasing decision. This is a big reason why I like thrifting and eBay, because the cost of adjustments is fixed and will more than likely need to be done on most items you buy. The cost of a garment though is highly variable.
As for how it changes the flow of the pants, I wouldn’t say they’re less comfortable to wear. Frankly, they’ll fit better to your body.