One of the big points in that article mirrors your example. The correct response is to allow the user to decide.
"But targeting the other program in such a way is no different than someone installing two A/V softwares. Sure they may conflict in some areas"
"This software program conflicts with this software program. You can choose to run them both and accept the problems that occur accordingly or you can choose to cancel this installation or remove program X"
Do you want to cancel, remove program X, or cancel the installation?
Give users the option to opt-into using your software, don't force users to get into a proxy battle by automatically opting into things.
"But targeting the other program in such a way is no different than someone installing two A/V softwares. Sure they may conflict in some areas..."
No. Hell no. Antivirus programs conflict for a good technical reason. NoScript and AdBlock conflict because the author of one dislikes the effects of the other program; were it not for that, the two extensions would be completely compatible with one another. Equating these two things with each other completely misses the point.
I'm giving an example of a way to approach this problem. Installing Noscript could add a rule to an Adblock whitelist. What Noscript is doing by trying to sneak it in is wrong. If they wanted to overwrite a rule, let the user do it. As that article points out, and as Mozilla points out, making that the non-default option is very important.
"But targeting the other program in such a way is no different than someone installing two A/V softwares. Sure they may conflict in some areas"
"This software program conflicts with this software program. You can choose to run them both and accept the problems that occur accordingly or you can choose to cancel this installation or remove program X"
Do you want to cancel, remove program X, or cancel the installation?
Give users the option to opt-into using your software, don't force users to get into a proxy battle by automatically opting into things.