I am not sure how much I can help you with your first two questions, but let me help you with the other three. There is no need to use the SimBiology Desktop, if you do not want to. The desktop is just a place where you can find examples. You can use the examples also from the command line. The examples all have a name with the ending .sbproj. If you want to load one of them from the command line simply use the following kind of syntax
sbioexample=sbioloadproject('Goldbeter_Mitotic_Oscillator_with_reactions.sbproj')
If I understand you correctly you are used to programming in MATLAB. Most things you can do programmatically in SimBiology you can also do via the Desktop and vice versa. Not everyone who would like to do modelling is familiar with programming and for these kind of users the Desktop is really helpful. Even if you are good in programming you might want to use the Desktop in order to get a nice diagram showing the pathway you were modelling. In order to export a model from the SimBiology Desktop to the command line simply click on the right triangle next to the navigation panel and select Export to Workspace.
It might be also good to keep in mind that "A project saves related models, tasks, and data in a project file with an .sbproj extension." (see Documentation about .sbproj files)
Have you been on this webpage SimBiology project page ? There you can find a link to (free) Webinars, of which some are longer than 45 min and much more.
On this page MathWorks Support you can find links to useful resources that can help you, among them a page to contact Technical Support. Please do not hesitate to contact Technical Support if you need help, have enhancement requests etc..
I hope this helps.
Ingrid