A club cannot be promoted to J3 unless it holds a J3 club license.
This is clearly stated on the J League official website.
https://www.jleague.jp/news/article/24405/
If the clubs ranked 2nd or higher in the JFL have not received a club license decision to join the J.League, clubs ranked 3rd or lower will not be moved up.
https://www.jleague.jp/news/article/26118/
Items related to average attendance and finances assume that the club holds a license.
It is an unspoken fact that corporate clubs such as HONDA FC, Sony Sendai, Maruyasu, and MinebeaMitsumi do not wish to be promoted from the JFL. However, we won't know in 50 years.
But I'm not sure whether that implicit fact should be set as an in-game setting.
https://twitter.com/Honda_FC/status/1166156856206610432
HONDA FC's official Twitter has hinted that they have no desire to be promoted.