No I dont use the right-click menu... that would involve moving my hands off the keyboard! Here are the steps:
1 Hit pause/break to bring up findrun
2 Start typing name of program
3 hit number key (FindRun goes away)
4 While program is launching, hit Pause/Break
5 Start typing name of second program
6 hit number key (FindRun goes away)
The problem is that from steps 3 to about 5, the other program is launching. In the middle of step 5 the launched app suddenly and violently grabs focus requiring you to restart the process. There are a few times when I'll start FindRUn, start typing the name of a program, then remember something I wanted to do in another app. THis is where the keeping focus becomes an issue. However these times are very few and far between.
If you add the ability to hold down a modifier when launching an app, I wont complain, and it will be nice during those times when I know I will be launching a few apps in quick succession. My point was that sometimes the reason I start launching a second app is because the first one is taking some time to start. In this case, I wouldnt have hit the modifier, and FIndrun would already be minimized, negating your modifier solution.
How often does this happen? Not often, that's why I say I'm happy with having an option to make FindRun always retain focus. I also kind of like your four second timeout idea (FindRun can lose focus after being open for four seconds). This allows me the time to do a quick search (without being interrupted), but if I dont know the name of the file and my search takes a tad longer, I can bring up another window to find the filename, then open with FindRun.
HOpe that helps. Ask again if you still dont understand my convoluted process!