So the transparent logo going opaque and back to transparent is nothing new. Our custom written alert has a transparent "R&D" logo in the lower left corner that becomes opaque when a Sub comes in. Added to that, the R and D letters split apart, moving to opposite sides of the screen, revealing a "new / resub" message at the bottom center, then return to their normal positions and transparent at the end of the animation. Old example from a few years ago, quality is low, but it was the quickest clip of mine that I could find showing my alert :
https://www.twitch.tv/robanddan/clip/FrailRichOrcaStinkyCheese
This is all done in CSS. The rotating ManVsGame logo "could" be a looping video file playing back in the HTML Browser Source, with its opacity being shifted in CSS. OR it could be made transparent via a series of calls to the obs-websocket plugin slowly adjusting an opacity setting in one of its source Filters. It all depends on which was more performant overall.
As for OBS-Websocket and Alerts controlling scene changes, this can 100% be done. Please look at these clips where I utilize obs-websocket and a tablet control panel to switch scenes, but also auto-enable a video of a lower third panel, which then disables itself shortly after it slides off screen, effectively resetting itself. The text and emote graphic are part of a browser source that also auto-populate the area with the appropriate information.
https://www.twitch.tv/robanddan/clip/CrunchyFairPepperUncleNox
You also mentioned a "queue" system for alerts. Yep, done that too, using the Async.js library and its Priority Queue feature.
https://caolan.github.io/async/docs.html
Different types of alerts have different priority levels. Priority Order is as follows...
1: Subs of all types (new, resub, gifts, etc). Raids, Large Donations, Giveaway starting trigger
2 : New Follow
3: Big Host (brings in 50% or more viewers than what the channel currently has. If we have 100 viewers and they bring in 50+ its a Big Host)
4: Small donation, StreamGifts purchase, Humble Bundle purchase
5: Smaller host (less than 50% of the current live viewer number)
6: Alert of a Tweet mentioning our Twitter account
This bundles up similar alerts so they all trigger one after another in order of priority, rather than handling them as they all come in, and puts the most important ones up front, and the not so immediate ones toward the back.