I investigated this issue a bit more. As the smallest repro case I could find was just changing the view matrix before calculating the frustum, I checked when frustum culling was added to Defold. Apparently it was introduced in version 1.3.1. So after trying both 1.3.0 and 1.3.1 I got these results:
1.3.0: no changes to default.render_script → no lag spikes
1.3.0: altering the view matrix → no lag spikes
1.3.1: no changes to default.render_script → no lag spikes
1.3.1: altering the view matrix → lag spikes
I also tried different options of vsync, update frequency and swap interval as I saw there were some changes in 1.3.1 regarding those, but in all cases 1.3.1 is the version that introduces the lag spikes for me.