Dude, you're not getting it. Just hit the macro, trust me, it DOES activate it for ALL VSTi and VST fx. I just tried it. You only have to do it once per project (or do it every so often if you add new VSTs constantly). You never have to click anything again - smart disable automatically freezes any VSTs you're not using, completely offloading that CPU until they're actually playing. 0 latency, no wait times, no BS, it's the best "freeze" you will ever see in any sequencer. And it only takes ONE CLICK to activate for your entire project.
For automation, there are a bunch of different ways to do it. The easiest way is creating a MIDI Out, point it to your synth of choice. Right click on the slider, hit "Configure". Put "MW" as Full Name and Short Name. Controller should be "1" which is the Modwheel cc. Then, all you have to do is edit the automation for that slider at any point to control the modwheel automation for whatever synth it is pointing towards. You can of course save this configuration as a preset and call it up anytime.
To edit that stuff in the piano roll, just right click on that slider control and do the "Edit Events in Piano Roll".
You can use the MIDI Outs and configure them to ANY control setup too, which is nice, and since basically everything in FL can be saved separately you can take the Modwheel automation you wrote for a Pro-53 patch, and load it up as the Expression automation for a QLSO patch.