Most of these are added under the "Extended program configuration" section in the 0.1.1 version. The "Bored Timeout" option is to come under Utility -> Additional Options window but it is not implemented yet.
That and some other options can be changed at once by selecting Utility -> Write Optimal Configuration.
Thanks for your help! Link to the release is in the first post, below are links to particular files:
Download for BGIEE
Download for BGIIEE
Download for IWDEE
Download for PSTEE