There is no difference if you install ports or packages, or mix them....
The only defference is that packages will require less dependencies, as they don't have to be build from sources....
As an example i can mention deprecated cvsup..... to build it from sources you need ruby (if i remember correct), to install package, you don't need it
Also as mentioned above, ports will be up to date, wile packages, won't be that current
It won't affect your system, if you mix methods.
When port fails for me to compile i just install package.
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