Use-case: custom plugin or extended use of entries/categories/tags
I just started using Craft, so I still don't understand 100% the core, that's why I cannot decide which would be the best approach.


Welcome to the community! You're asking a lot here! 

Someone more knowledgeable about plugin-development will want to chime in here but in my experience, Craft is quite flexible and can handle a lot of things out of the box, even without writing a plugin. It's awesome when you have to relate content to and from each other, like you're wanting to do here.

I don't quite know all the requirements but if I were spec'ing this job, it sounds like you could do a lot of this by using most of Craft's entry types.


Jobs (section)
Companies (section)
Skills (Category / Source )
Industry (Category / Source)
...


I would deal with ATS import as a separate plugin.

You'd create entries in the Jobs section. Create fields that relate the job back to an entry in the company section as well as categorize it using those categories. Like entries, categories can have custom fields so you can put assets field on a skills category and upload logos so every job that has, say, jQuery in it, could have that logo appear. 

Depending on your requirements, your Jobs section could have multiple entry types. So if you have specific fields that need to appear on certain jobs categories and what not, you can do that. 

I see Matrix being an MVP here, too. When a regular set of fields doesn't cover what you need (you mentioned "custom settings that apply to each job"), you can mix and match a ton of different combinations with Matrix. 

Bottom line: I would play more with Craft before you get into plugin development. If you're new to Craft, how many sites have you built with it before you started plugin development? Is there something that led you to know you actually need to use a plugin or is it just a programmer scratching an itch? (We've all been there!)

When it comes to programming and web design in general, to paraphrase The Matrix, "there is a difference between knowing when to reinvent the wheel and not." That only comes with experience.