Michael,
Phonegap/Cordova allows you to wrap all of your web/app logic in the (more or less) the same JavaScript/CSS files your web browser would use into a package for deployment on iOS/Android. This means that your App does't need to download jquery.js or whatever each time as its there in your app.
The line starts to blur between what an App is or what a web app is to what a Web browser is. Until recently I understand that the Apple Store wouldn't allow you to download files for your app, however I understand that restriction may have eased.
Whilst you can do downloads from servers to your app, you will suffer if you are doing that every time as you are doing unnecessary downloads. On a local WiFi point this may not be that bad, but if you have limited mobile connectivity then you're in trouble. As an example I was using my own app (for testing) today and I moved from WiFi at home, to 4G outside to 3G as I got outside London to GPRS and Edge as I hit the pagan badlands of Essex. if I had to download js files through GPRS or Edge I'd slit my wrists now and get it over with :) Most of my code is in the app, most of the base data is in the app, I only call out to download specific and updated data, this means that the user gets fast refresh, and minimal download bills.
I'm unclear (because I'm not as clever as some of the people here) if you could even do some of the stuff you want to do with downloads, e.g. background GPS geo-location, barcodes, etc. These are provided through plugins and I've never even considered doing them through downloads. I wouldn't have thought you could but take my advice with a pinch of salt.
There are standard ways to get data from external websites to your app and to do error checking, See Angular promises for the background (no pun intended) on this (stackoverflow is your friend).
Your background in development will stand you in good stead. I've been developing since, gulp, 8 bit micros you brought as a kit, remember the Nascom-1 anybody. My very, very first program was written on a Heathkit 256 byte (yes 256B) hexadecimal development rig. I also have developed C compilers and written chunks of low level UNIX stuff, so I *thought* I knew development. JavaScript and Angular and Phonegap/Cordova are very different. JavaScript used to be a bit like C. Nowadays its very, very asynchronous (think signals and semaphores, locks and whatever you used to use or call). It took some time for me to get my head around it as people have come up with all sorts of new names for what we used to do with signals and async stuff in the 80s. Some low level stuff is really well abstracted away but some stuff is a nightmare as the names have changed and the patterns insist you work this way or no way. I'm sure other people have their view on things, but thats my view as a old-school C hacker. There's also a major problem in that lots of people write stuff up for the Internet thats very specific, and often not quite right. The signal to noise ratio is way too low for my liking, Too many small pages with lots of ads and little real usable up to date content.
JavaScript/Angular/Phonegap/Cordova is/are also nice to use, but you have to get used to the patterns that people/systems/processes want/need/demand to use. The syntax for Angular stuff makes Lisp look really neat and tidy IMHO, it tends to mean that you have long files and the abstraction of services/controllers/UI is nice but sometimes gets in the way. Its taken a long time (circa six months) to get used to the way of working and to find a workflow thats good for me. You will have that learning curve to go through.
My suggestion is to start with the simple docs and build a dead simple app. Its quicker to build a simple one first and then do a more complicated one rather than jumping in at the deep end with the complicated one. The act of building a simple app that gets some JSON data from a server and displays it on multiple screens is really useful and powerful. Also consider the use of a framework to ease some of the work. I use Ionic as it was suggested to me and as I'm not very bright it was easy to learn. However the more 'stuff' you layer in, the more issues you may face. Take your time and learn. I have read a lot of stuff but I do wish there were more paper manuals around, however the delivery cycle for a book means the subject matter is often out of date buy the time the book is printed. People on this group will take the time to answer your questions if you frame them well and show that you have done your homework. Bland questions such as "it doesn't work, help" get little response, though sometimes the responses are witty as well as pointed (if you are lucky).
Hope that helps, start reading, write the first simple app and learn,
Best wishes,
Rob