why cant you run the package 3 times?
Just run dtexec with /config and Specify a configuration file to extract values from
Or you can create a sql job with 3 steps and on each step run the same package informing different config files on the configurations tab.
I really don't see the problem. "Package" and "config file" are two separate things. Inside BIDS, if you disable configurations, and run the package, it wont read any config file, of course, but if you enable, it will read the values from the config (file or server or whatever) and use them even if you have different values set on the package.
So, why cant the developers work with the configurations enabled and have the values the need set on the config files?
EDIT:
I think you missunderstood. From the page you posted:
1- The utility first applies the design-time configurations.
- that means, read the configurations on the config file
2 - The utility then applies the run-time options that you specified on
the command line when you started the utility.
-that means, things like setting a variable values using the /set option on dtexec
3- Finally, the utility reloads and reapplies the design-time
configurations.
that means, reload the configurations on the config file
that's why you read in several places that in SQL Server 2008, you cannot use /Set option to override values that are also set by a configuration.
It doesn't actually mean you cant, it means that the values on the config file will prevail over any value set by command line.
No worries, at no moment the values set in BIDS will overwrite the ones you set on your config files.