This is a great question! What is the stem of a noun? How do we define the stem of a noun?
Let's start with some vocabulary.
The base of a noun is the form we get when we drop the genitive singular ending. So the base of θύρᾶ, θύρᾶς is θύρ-.
The stem of a noun is the base of the noun plus its characteristic vowel. So the stem of θύρᾶ, θύρᾶς is θύρᾶ-, since the characteristic vowel is ᾶ.
These definitions of "base" and "stem" are consistent in both Latin and Ancient Greek.
We get the base of a noun by dropping its genitive ending, and we get the stem of a noun by adding its characteristic vowel to its base.
Now, in the first declension of Attic Greek, there are two large categories of nouns: ᾶ-stems and η-stems. θύρᾶ ("door") is an example of an ᾶ-stem noun. έπιστολή ("letter") is an example of an η-stem noun.
One of the nice advantages of having the word "stem" (in addition to the word "base") is that we can categorize nouns according to their stem. For example, some first declension nouns in Attic Greek are ᾶ-stem nouns, and some are η-stem nouns.
It's a little difficult to categorize nouns according to their base, isn't it? For example, the base of θύρᾶ is θύρ-, and the base of έπιστολή is έπιστολ-. But how can we create categories from these bases?
We can categorize nouns from vowel declensions according to their stem vowel. Some examples are ᾶ-stems and η-stems from the first declension, and ο-stems from the second declension.
Getting back to your question, I think that the key insight is understanding the difference between a base and a stem. The base of a noun is the form we get by dropping the genitive singular ending. The stem of a noun is the base of the noun plus its characteristic vowel.  
In Attic Greek, first declension nouns often have stems ending in -ᾶ or -η. The base of θύρᾶ, θύρᾶς is θύρ-, which we get by dropping the genitive singular ending. The stem of θύρᾶ, θύρᾶς is θύρᾶ-, which we get by adding the characteristic vowel ᾶ to the base.
 According this definition of "stem", we can say that if a noun does not have a characteristic vowel (a stem vowel, that is) then its stem is identical to its base.
 Words like θύρᾶ, θύρᾶς have a stem vowel of α. Words like έπιστολή, έπιστολῆς have a stem vowel of η. What about words like θάλαττα, θαλάττῆς, which have a stem vowel of α in some forms and a stem vowel of η in other forms? We can say that words like θάλαττα, θαλάττῆς have a hybrid stem. One theory about the first declension in Attic Greek is that it started off with one set of endings (α endings) and then native speakers started to substitute η for α in the endings of some words because it was attractive to them, or convenient.