Besides factoring out a factor of $4!$, we can also factor out an additional factor of 4.
First, label the upper-right-hand box as $a,b,c,d$.
a b * *
c d ? ?
& ? ? ?
& ? ? ?
There are of course $4!$ ways to choose the values of a,b,c,d. Now the * signs must be c and d, and we can assume by switching the last two columns that they are in this order. Similarly, the & signs are b and d, and we can switch the last two rows to get them in this order. We've extracted a factor of $4$ by switching the rows and columns in this way, and we're left with
a b c d
c d ? ?
b ? ? ?
d ? ? ?
One can now simply check that
a b c d
c d ? ?
b a ? ?
d c ? ?
has two solutions and
a b c d
c d ? ?
b c ? ?
d a ? ?
has one, thus there are in total
$$
4! \cdot 4 \cdot (2 + 1) = 288
$$
solutions.
$$
* \quad * \quad *
$$
Note 1.
This problem is closely related to the the problem of counting Latin squares.
The reason this is relevant is that counting the number of Latin Squares of order $n$ is a very difficult in general, having only been calculated up to $n = 11$.
Intuitively, one expects the number of Sudoku boards (of any size) to be similarly hard to compute, and sure enough, the problem is quite difficult: see here, here, here, and here for some references.
Note 2.
Interestingly, the number of $4 \times 4$ Latin squares is 576,
which is exactly twice our above calculation of $288$.
In other words, if you try to generate a random "Shidoku" board by just ignoring the boxes and dealing only with rows and columns, there's a $50 \%$ chance you'll end up with a valid board anyway.