Unless you are familiar with git (or eager to learn), I would recommend the “Full Package” install, with the manual modifications after the fact (as you initially described).
The error messages you linked to can be avoided by disabling PHP Strict Standards and disabling deprecated warnings:
If you want to transition to Git, you’ll want to checkout the git commit which best corresponds with your install. If you installed OJS 3.0.1 from the Full Package, that is probably the git tag ojs-3_0_1-0. You’ll want to resolve and commit any differences between your intentional changes and that checkout in both the application and the submodules (lib/pkp, for example). After that, you should be able to rebase the application and submodules.