I saw a sentence
Tu femina non es, sed puella es.
My understanding is,
Tu non es femina, sed es pulla.
is also a correct sentence.
If I write this as
Tu non es femina, sed puella es.
or
Tu femina non es, sed es puella.
Are these sentences awkward though syntactically correct?
The first two examples have the same order of the verb and the noun in the two clauses, but the last two examples have different word order in the two clauses.
Yes, all these sentences are correct. There is no rule whatsoever that says that two adjacent sentences, or two main clauses coupled with sed, or whatever, need to have the same word order. On the contrary, Latin writers will often vary the word order, presumably to draw out a contrast, or because for some reason it sounded better to them.
For example, Cicero In Verrem 1:
... actor accessi, non ut augerem invidiam ordinis, sed ut infamiae communi succurrerem.
I came as plaintiff not to increase the ill will against the order, but to prevent our common disgrace.
Therefore, there is also nothing "awkward" about your examples; however, all your sentences seem a little stilted to me anyway. If the verb is the same, it is very common not to repeat it, e.g.
etc. You could also say: Puella es, non femina.
Using the same word order in two parallel phrases or clauses is unmarked (standard). But word order is rather free. When you 'deliberately' or conspicuously switch the word order between two parallel clauses or phrases, that is often considered chiasmus, a figure of speech.
Tu femina non es
sed es puella.
Chiasmus is a crosswise arrangement, like the letter chi (X). It is so called because one can draw a X between the two lines, if one connects noun to noun, and verb to verb.
