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I have noticed in several professional documents (templates, guidelines, co-workers' projects, etc.) the designer has adjusted the opacity of certain elements to get the desired colour.
Is this best practice for designing?
In my opinion, changing the colour of the element itself (when possible) would be the better practice, since you can visibly see the exact colour you enter (hex, rgb etc.)
Changing the opacity can always be tricky, especially if you're planning to save your work as PNG file and use it in web design (elements that are below your graphic will be more or less visible).
Changing the color always was and it will always be the safest way of playing around, no matter you're designing for web or print. On the other hand, playing with opacity it's the only way of obtaining certain effects. I guess each designer should know the final purpose of their work and apply one of these two options accordingly.
You're right, technically for print it's a better practice to change the color of the element than transparency in most case, unless the transparency adds something to the design. But that is if you like to be certain of the color you'll get once your file will be printed. For web, it matters less.
The reason why designers often prefer to use transparency is because it's easier for them to improvise with their design and play around until they get the "desired" effect. Since Adobe fully released the transparency effects in vector and when InDesign came out, it almost became a way to create.
It's possible that some designers who have prepress experience from the early 2000 will prefer the control of using the exact color instead of transparency because of the full control on the results (and reliability of this method*) while the designers who started learning graphic design with Illustrator 10, Photoshop or InDesign (or embraced it) will prefer using transparency for practical reasons. Sometimes, designers will do their designs with transparency during the creation process and then convert some transparency in their design to exact colors.
In both case it's really a question of preference, "comfort" and priorities.
*and because they lost half their hair and sanity "ripping" the new InDesign files full of transparency when it came out
