I do think we're exactly on the same page, when it comes to how mods should be treated, the only difference is, I see real issues with microtransaction-type fodder MODs, created not by the current enthusiasts, but by the new influx of 'MODers' (I'm still not sure what the correct English phrasing for a MODer is).
Look at early access. It's become overgrown with easy cash projects. Once we start treating MODs like APPs, we'll start paying left and right, €/$0.95 for a new weapon. In no time, we'll be overrun with APPS, instead of MODs. MODs are things people put their soul in, with the knowledge that they would likely never see a return. I simply fear the effect will run way out of bounds.
And I'm not naive enough to consider for even a second, that Valve is capable of keeping this in check.