Yes, Universal can make any Marvel type of character regardless if they're from the comic books or from the MCU. The 1994 contract doesn't discriminate between comic and movie versions, so as long they're Marvel characters, they get to use whatever version they need for the attraction. Marvel itself must approve new attraction proposals and Disney can't do anything to interfere with it, just "because" they'd have to have a valid legal reason like hurts the brand/story, etc or that it would hurt Disney more in terms of attendance and profits at the expense of the competitor. Marvel had to sign off on the upgrades to the Incredible Hulk Coaster last year, so there's an example of the contract in action. Below is the excerpt from the contract about this.
- "i. [Marvel/Disney] will reasonably cooperate in making information, artwork, archive material, key personnel, etc. available to [Comcast] in order that [Comcast] can creatively develop THE MARVEL UNIVERSE and exploit its rights hereunder. [Comcast] will reimburse [Marvel/Disney] for its reasonable costs in this regard, including time of non-executive personnel and their reasonable travel expense.
- ii. Whenever [Marvel/Disney] has “reasonable” rights for rejection of approval hereunder, the basic criteria to be used by [Marvel/Disney] may include inconsistency with (i) basic story line, (ii) the powers, (iii) basic personality traits, (iv) physical appearance (including clothing or costume), and/or (v) living habitat or environment relating to such character as portrayed in [Marvel/Disney]’s exploitation of such character in comic books or other products for the particular time period being depicted by [Comcast]. iii. [Comcast] shall take appropriate action, as directed by [Marvel/Disney] to protect all copyrights and trademarks in connection with the uses granted hereunder, including in-park uses, merchandise and packaging."
The key word underlined in number ii is "other products", so to answer your question, yes it includes those from the MCU. Apparently, I heard a rumor that Stan Lee wanted to keep the classic comic book-style of Marvel Super Hero Island because he said Marvel started from the Comics and wanted the guests to realize that it originated from the comics, not from the movies. As for the link, here you go.
Marvel Agreement between MCA Inc. and Marvel Entertainment Group