Is your BG thin enough so that your U shaped fitting for the intake/return can fit over it? If so you can run those over the BG but then put your little suction cops holders on the side glass panel. So in other words the tubes come from over the back, but are held on by the cups on the side. Sometimes that works well. Just depends what type of lids you have though, some lids don't allow for that much movement for stuff coming into the back of the lid/hood. If that doesn't work then you can do like you had in mind and put some silicone on the holders and that should hold them to the BG. Just put some pressure on then while they dry so it adheres well.
I was also thinking I could maybe take the suction cups off of the u shaped piece and pierce them through and then attach them to the glass as normal, I have a few clips that are much longer, at least I have a few ideas on why to do now so I’ll just go with the best option when I buy the background.
On another note these backgrounds don’t discolour or anything do they?