Gowdas and Shettys are prominent and also dominant communities in the state of Karnataka. Where do these communities belong in the Chaturvarna System?
I have no idea about the Gowdas.
As regards the Shettys, they belong to the Vaishya Varna as per the Chaturvarna system.
The word Shetty is derived from from the Sanskrit word Shresthin (श्रेष्ठिन्), the same source gives rise to Seth (सेठ) of North india and Chettiar (செட்டியார்) of Tamil Nadu. They were traditionally merchants and engaged in the money lending/ banking business. Occasionally the term could also be used to mean the chief of a merchant guild.
There are many references to the money lending business in Kutilya’s Arthashastra as well as copper plate inscriptions of kings which I’m not aware about.
As per this research paper they belong to same genetic group. So dna is 100percent same. https://www.researchgate.net/publication/5547814_Genetic_variation_and_population_structure_of_interleukin_genes_among_seven_ethnic_populations_from_Karnataka_India
It is impossible to answer this question from the practical point of view.
According to the aptitudes resulting from the dispositions of Nature (Gunas) and works (Karmas), the social order of fourfold division has been created by Me. Though I am their originator, know Me to be not an agent but the spirit unchanging.
You will have to know the Karma and Guna of the past life of every person in these communities. That is clearly impossible.