If I were to work for a Japanese company as a “full time” contractor does all the visa requirements still stay the same as a regular full time employee. Like for PR or highly skilled foreign professional visas. Can’t really find much information on contractors specifically online. The company has a lot of remote workers in other countries so everyone is being contracted instead of being full time employees.
My assistant called the 外国人在留総合インフォメーションセンター about your question, and this is what they said (paraphrased):
A company can sponsor a visa for full-time contractors (契約社員) if they are paying enough salary (officially it has to be as the same amount as an average college graduate). A company can not sponsor a visa if they are hiring someone as a freelance contractor because there might be chances that they can get jobs from other companies.
The point is that a company can only sponsor a visa when the person is only working for the company (the person belongs to the company), as the company is submitting all the company information to prove “we are the company which this person is working for”.
When they can be sponsored, and they have enough points (over 70 points) on the point calculation visa, they are eligible for a Highly-Skilled Foreign Professionals visa, but normally, if the person is an engineer or developer, they get a Engineer/Specialist in Humanities/International Services visa.
Based on this, it looks like there shouldn’t be any issue from a visa perspective with the company hiring you as a contractor instead of a regular employee.
The topic of freelancing is a bit more nuanced than they seemed to imply, but I don’t think it is relevant to your question (as you’d be a full time employee).