For the first/focus issue:
When I use a hotkey to trigger a capture, then press a numeral to select a pre-defined area, then give the left mouse button a single click to capture, the focus stays on whatever application had the focus in the first place. This is true whether using MindManager, Chrome, Irfanview, or even the desktop with all apps minimized.
Here's the tricky part: This only happens when I am capturing an area within the active application. If Chrome is active, for example, but not full screen, and I place my cursor over the empty desktop beside it, and capture an area not including Chrome, the focus does shift to the capture dialog. Same actions, however, with the cursor over the active application and the capture within that window, and the focus remains on the active app.
If I do an area capture with a click and drag, there is no problem. The focus moves to the capture dialog.
For the Save issue: Looks like my original strategy will be best: Click the Save to Clipboard button (setting it to default to saving the image), and do a Save As. The Save As does keep consistent in the folder it uses, so once I change it, it stays.
Hoping this winds up being helpful!