When you set the font for a specific channel, that's the font for that channel. If you check the box "set as default", that font will ALSO be used for all channels for which you haven't set a default yet. If your default channel font is Fixedsys, and you go to #channel1 and set that font to Tahoma but also check the box to make that the default font, all #channels will use Tahoma unless they previously had a font specified for that channel. If #channel2 is still using Fixedsys, that's because you had previously defined the font for #channel2, even if it was defined to be the same as what the previous channel default had been. If you go into #channel2 and open the font dialog there and check the box "use default", #channel2 uses whatever the channel default is, and changes when the channel default is changed.
The font for the Status Window is separate from the font for #channels. When you change it, that's the font for all Status Windows as well as the font used by @custom windows you open later without specifying a font. If you check the "Use Default" box in the Status Window, it goes back to the default font for Status Window, which for me is Fixedsys.
If you use notepad to look at your mirc.ini you can see these fonts defined in the [fonts] section. (Look but don't save changes to mirc.ini using notepad) "fstatus=" is the line defining the default font for the Status and @custom windows, "fchannel=" is the default font for #channels that don't have one defined for them. If you see "f#channel2=", that shows you've defined a font for #channel2 which won't change whenever the "fchannel=" default channel font is changed. You can also set a font for the Scripts Editor window, and it will be shown in this section on the "fscripts=" line. "fwwwlist=" is a font defined for the alt-u url window. "flist=" is the font defined for the /list window.