Yes, as seen below I have alternating colors and conditional formatting:
How to have both:
1) Create the conditional formatting for the list:
a) Format this column
b) Go to Manage Rules > Add Rule > Make the rule and formatting you want.
2) Format the current view (for alternate coloring of rows)
a) Go to All Items > Format Current View
b) Add the JSON code:
{
"$schema": "https://developer.microsoft.com/json-schemas/sp/view-formatting.schema.json",
"additionalRowClass": "=if(@rowIndex%2==0,'ms-bgColor-themeLight','')"
}
c) Click Save
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