Got it about the customization. But while it has a benefit to you as a probable "power user", it has a cost: beginners don't get it. They don't understand why part of skype is in a windows while another lives in another. When widgets are dockable/undockable, they undock by mistake, lose the undocked widget in some unseen corner of their screen, are unable to reattach it, and get frustrated.
"All-in-one" UIs allow for less customizability/rearranging, but IMHO that's a trade-off they do for one huge benefit: simplicity.
With this in mind, how do developers decide which direction to push? By looking at their target user base, of course. And the target user base of Skype is not mostly savvy professionals who like to rearrange windows/widgets, it's humans wanting to talk to other humans. So Skype developers naturally push towards simplifying.
Other examples of applications who are kinda, in various ways, reducing such customizability:
- Office, with the Ribbon: no more detachable toolbars.
- All iOS / Android apps: single-screen, one thing focused at a time (with the exception of left/right tiling in recent iOSes)
- Even the GIMP introduced a Single Window mode in recent versions.
Now, why don't Skype developers let users pick whether to choose single or multi-window mode? (which they used to do in the Qt-based version under Windows, see the "View" menu).
- Because configurability means more code, more tests, more bugs, more money. So if only a tiny part of the userbase requires the configurability, product managers bring the hatchet.
- And again, options means beginners will accidentally change them to the one that doesn't fit them, won't understand what the hell happened and how to change it back, ending up either grudgingly accommodating to the undesired option, or getting frustrated and leaving.