Either approach would work fine and neither should be affected by upgrading MODX. You should never, ever, modify the actual MODX core code (what's in the core and manager directories). It's relatively easy to create your own classes that extend the MODX classes if you need to add fields.
Generally your code, when installed, will go in core/components/
componentName/ or assets/components/
componentname/, so it will be completely independent from the MODX code.
Putting the code in a single or multiple packages shouldn't make any real difference unless the packages conflict with each other. There may some advantage to putting them all in one package, though, since every package gets its own namespace. If they all share a single namespace you won't have to remember which namespace goes with which package and you can also share any lexicon files between them. See the Login package for an example of multiple functions packaged together:
https://github.com/splittingred/Login
The method in my tutorial is geared to creating xPDO classes where you have one or more unrelated tables. It just saves you from having to create a schema and provides a convenient way to generate both the schema and the class and map files. If you'll have related tables and intersect objects, you'd have to rewrite the schema to include them (though I think I'd probably still do it my way and just add the related objects and aliases to the schema).
All that said, If I were in your place, I'd use MyComponent to create the packages. It's a little difficult at first, but once you get the basics and the workflow down, you can create a new package in very little time. I can create a completely new package in about 20-30 minutes at the most (not counting writing the code, which you have to do with any method).
Let me also recommend PhpStorm if you don't have it already. It's very easy to make an entire MODX install into a project and do your own work within it. MyComponent puts all your work in assets/mycomponents/
componentname/. PhpStorm will know about all of your classes and all of the MODX and xPDO classes (and all their methods) and will autocomplete any of them and give you argument hints. It will save you a ton of time and will pay for itself in less than a week. As an example, I can type $modx->makeUrl(), put the cursor on it and type Ctrl-b and PhpStorm will open the the MODX file containing that method and put the cursor on it in about a second -- Ctrl-Alt-left-arrow will take me right back to my own code.