Consider the following two utility functions:
$EU(p)=\sum_i u_ip_i$
$EU^2(p)=(\sum_i u_ip_i)^2$.
In preference theory, $EU$ and $EU^2$ are equivalent because they represent the same preference. A preference is a complete and transitive binary relation over the set of alternatives.
However, obviously, in likelihood-estimation with logit/luce choice rule, $EU$ and $EU^2$ give different probabilities. For example, the probability of choosing $p$ over $q$ can be:
$L(p)=\frac{EU(p)}{EU(p)+EU(q)}$
OR:
$L(p)=\frac{EU^2(p)}{EU^2(p)+EU^2(q)}$
That is, for exactly the same preference, two different likelihood functions are viable.
How do econometricians justify the usage of $EU$ instead of $EU^2$?
Related questions:
Does concavity of the utility function has any bite?
When can one safely talk about decreasing marginal utility?
The related posts are about cardinal utility or the strength of preference. However, those arguments cannot be simply applied here because:
The "cardinal utility" applies to the lower case $u$, which is unique up to an affine transformation, but it does not apply to EU as a whole, which is unique up to a positive monotonic transformation.