It would be nice to have a menu choice to save just the entries for the actual channels without saving everything else. If there are N channels open, then it would create/alter N items under the [windows] section.
When I used the upper left menu of a channel window to make the choice position/save-all, I was expecting it to create N [windows] entries to save all N currently-open channel windows. Instead, it created a pair of entries for each channel plus a pair for a lot of other things, including all the open @windows including @debug. It creates an item for @windowname as well as for @windowname-networkname. It's reasonable to expect that 'all' in the channel menu means all channels, and possibly the status window too, but not for all the other entries for all @windows, as well as wdccs* or wdccg if there happens to be an active dcc in/out at the time.