I found two articles, both on Tetris.
The first one is Tetris is Hard, Even to Approximate by Erik D. Demaine et al. It uses the unary encoding scheme for 3-Partition problem and constructs a polynomial reduction:
The $a_i$'s and $T$ are represented in unary, so the size of the game is polynomial. (from Theorem 3.2, page 9)
The other one is Tetris is Hard, Made Easy by Ron Breukelaar et al. It also uses the unary 3-Partition problem:
Note that the board is constructable in polynomial time (measured in the
input size), since the variables in the problem definition may be given in unary
due to the strong sense of NP-completeness (Theorem 1). On its constructibility,
consult . (from section 2.3)
I did not go into the two articles. Are them qualified to your references request?
EDIT: I recently found another example of optimal scheduling of a job system with ordered precedence constraints on two dedicated processors. Here is the paper "On the Complexity of Scheduling Problems for Parallel/Pipelined Machines" (IEEE Transactions on Computers 1989).