Universal has had a special contract with Star Wars merchandise before Lucasfilm was bought out by Disney. Same with Marvel and DC...the thing about these properties is that their merchandise and the actual intellectual properties are two different things. You can get the rights to sell merchandise, but not necessarily make rides or have costumed actors walking around. So if Universal has a deal to sell Star Wars stuff, that doesnt really infringe on Disneys ability to make a Star Wars ride. Thats because merch is typically not released by the studio/owner of the IP, but a manufacturer who has worked out a deal with the property. Universal is getting these goods from that manufacturer, not Lucasfilm, DC, etc.
Same with I Love Lucy...that store used to be filled with Lucy stuff but has slowly been overtaken by Betty Boop; thats not because of any falling out with I Love Lucy (the exhibit still exists, obviously), but rather an issue with the company issuing the Lucy merchandise--I think they just shrunk and couldnt keep up with Universal's orders leading to a diminishing selection of Lucy merch, but Im not positive.
So look at it this way--Iron Man toys arent made by Disney, but by Hasbro or Mattel or whoever. Universal and Hasbro dont have any issues...so the merch can be sold through them with the right contract. Thats how the Terminator store works, in simplified terms.
By the way, this stuff is usually marked up a bit to handle the fee Universal has to pay for bringing in this merch from out-of-house...I believe Star Wars shirts are about $3 extra a pop.