The issue is that I want the welcome page to have different permissions than the remaining pages on the site. I thought I could break inheritance and then create unique permissions. After breaking the permissions and changing the groups it affected the entire site. Is there a way to make the welcome page ONLY unique?
An aspx page is just an item in a list technically so applying unique permissions to this page shouldn't theoratically affect the site permissions. All users will need read permission alteast to the welcome page to be able to access the site. It is like a door to the house. You can use JSOM/REST api on your welcome page to check who the user is or is user in a certain group and redirect different users to different welcome pages if that is what you are trying to achieve