Hi, no problem.
#3 would see you incorporating Node-RED into #2. But Node.JS, as stated, is a micro-services architecture tool. So you can run many Node.JS services in parallel. They could talk to each other via many different means that both Node-RED and raw Node.JS services support: UNIX pipes, UDP, TCP, Websockets, MQTT being the ones that come to mind, there will be others as well no doubt. A simple way would be to treat Node-RED as an entirely separate web service (it doesn't matter that it may run on the same Pi). In this case, you would use one or more http-in/out nodes to define a REST API. In your Node.JS service, you would call to the Node-RED URL's using http requests and get back some JSON from Node-RED containing - for example - the results of a MongoDB query. Sorry, I don't have an example of this to hand, not sure many people are doing that to be honest since it is generally easier to stick with just Node-RED. But it is a viable option and would allow you flexibility in the future since you could move either of the services to a different device very easily.
Using Kendo UI does not, as I understand it, restrict you to using a Node.JS service since it is a front-end library not a service. You could equally well use it with uibuilder which should be a lot simpler. You would simply download the Kendo UI components into the ~/.node-red/uibuilder/<instance URL>/src folder and access them from there in the same way as the default template for uibuilder loads the index.js and index.css files. Alternatively, if Kendo UI is available on npm, you could install it, add it to the list of installed components in settings.js under uibuilder.userVendorPackages.
In terms of which version of Kendo UI to use, my personal recommendation would be to use Vue if you don't already know one of the other frameworks. It seemed to me to be rather easier to learn. REACT would be my second choice. I don't like Angular, it is far too complex and restrictive for anything but the most complex app.
As mentioned before, you might not even need Vue/REACT/Angular. Especially as you are using Kendo UI, you might well be able to get away with just using JQuery which uibuilder already makes available to you. I would only go for one of the others if you had a very complex UI to build as a single page app or perhaps if you needed a reasonably complex UI that took lots of user input. All will be served fine from a Pi, where you might struggle is using something like Angular with the browser on a Pi or when consuming Angular from a mobile device. Honestly though, if you are worrying about this from the outset, you probably have bigger problems to resolve.
In terms of keeping the front-end "vanilla" and working with others, that might change the dynamic slightly though you only really need to convince them that Node-RED makes a useful service platform. To be honest, Node-RED only makes sense either when you need rapid prototyping or you have limited programming skills. Otherwise, Node-RED brings a lot of baggage that you could avoid if you have other developers to create a custom back-end. When I say baggage, that isn't to put down Node-RED in any way but it is a complex set of moving parts, like a Citroen 2CV in a formula one race, Node-RED is not always the answer.
It is really hard to give further advice without understanding more about your requirements and the combined skills of your team.