“Biological sex” has no agreed upon meaning.

There is scientific evidence to counter Trump's Executive Order.

First, according to Trump's Executive Order:

Sec. 2.  Policy and Definitions.  It is the policy of the United States to recognize two sexes, male and female.  These sexes are not changeable and are grounded in fundamental and incontrovertible reality.  Under my direction, the Executive Branch will enforce all sex-protective laws to promote this reality, and the following definitions shall govern all Executive interpretation of and application of Federal law and administration policy:

(d)  “Female” means a person belonging, at conception, to the sex that produces the large reproductive cell.

(e)  “Male” means a person belonging, at conception, to the sex that produces the small reproductive cell.

Presented next is a well thought out discussion on Quora by Jae Alexis Lee. The discussion counters how "Sex shall refer to an individual’s immutable biological classification as either male or female" as stated in (Sec. 2-a) of Trump's executive order. The assumption is incorrect; read on. 

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Quora:  Biological sex” has no agreed upon meaning.

Intersex Symbol

This is a problem with the vocabulary and taxonomy advanced by anti-science bigots who attempt to distill sex and gender into a binary model. It breaks when you try to talk about things that aren’t binary and you have to go through increasingly complicated mental gymnastics to enable the model to exist. It’s far easier to be precise about what you mean. [

Intersex refers to a large number of uncommon combinations of sexually dimorphic characteristics. [It is established that  1.7 percent of the population are born with intersex traits]. As an example, XX chromosomes are commonly associated with female gonadal development and the development of female primary and secondary sexual characteristics. XX individuals with an SRY gene, however, will develop male secondary sexual characteristics but will also be sterile. If we define sex on the basis of gamete production (the producers of small, fast moving gametes are male and the producers of large, slow moving gametes are female) then an SRY positive XX individual is “biologically neuter.” They don’t produce gametes. [Producing neither large or small reproductive cells].  

If we define their sex on the basis of external genitalia, they are ‘biologically male’ because they tend to have a fully developed penis. If we want to be bigots who think every XX individual is female always and every XY individual is male always than the XX person with an SRY gene is ‘biologically female.’

And that is the problem with the assertion that someone is “biologically male / female.” We don’t have an agreed upon definition for what that means. Is it about karyotype? Gametes? Genitalia? Hormones? Self perceived identity?

Does it matter? [now it does]

This question asks about genitalia but there are a number of intersex conditions that result in ambiguous genitalia. How do you classify those using a binary model?

The world isn’t simple. It’s complex. Culturally, we crave simplicity. We like simple answers. We like definitive taxonomies. We like certainty and we like to be able understand. Sometimes, understanding is hard. It requires nuance, specialized language, research, and education that explores concepts with significant depth. Accepting that we don’t understand something is hard. Accepting that the model we’ve used to understand the world is insufficient to explain a new thing we encountered can be very hard.

Intersex people are intersex. If you want to classify them as male or female or something else, I would suggest that the only classification that matters is how the person identifies. [What a concept] Respect their identity and get on with life. The specifics of their medical details are only relevant to their health care providers and health care providers need to treat the whole person, not just decide if they treat a person as ‘male’ or ‘female.’

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My Note Again:  If you really want to get into the weeds, read the Scientific American article "Sex Redefined: The Idea of 2 Sexes Is Overly Simplistic".