The only way to really achieve that with ISBoxer is to create some mapped keys which trap those button clicks and only sends them to the active window (Window:Current). You can do that with a Straight Key Broadcast, and make sure you set the Target to be Window:Current.
Then, you just permanently enable Mouse Broadcasting, which is actually a little tricky because if you turn on the normal broadcasting it turns off mouse broadcasting when you turn it off, so you need to adjust the ISB42 - Toggles -> Activate Repeat (current window) mapped key so in Step 1, you select the second action and untick the Mouse repeat option, and in step 2, you select the first Action and untick the mouse repeat option.
Then under repeater profiles -> default, you can set the Mouse Repeat Enabled.
Now, if you might actually want to enable/disable broadcasting and have your mouse clicks go to all windows at the same time (useful for setting in game options, logging in, doing certain other interactions with NPC's and stuff, then you might actually want to put the mouse trap mapped keys into their own keymap, so you can disable/enable that Key Map at certain times, like maybe you want to enable broadcasting and have it actually do some mouse repeating, and perhaps not trapping the mouse buttons. You could add some Key Map State Actions to the broadcasting toggle for that.
Or if that is sounding a bit tricky, then there is always
this video for gathering, which shows several pretty slick setups for using Interact With Mouseover (most people go for option 3).