you are a guest and one should offer a modicum of respect.
If I consider that display of temper or noise may be unrespectful during Nyepi, I am not sure to see what unrespectful is in doing a quiet jogging.
Also, when you are a legal permanent resident in a country you cease to be a guest.
I totally agree with
@dafluff and a few others: Forcing your religious practices on someone else who is not of your religion is never ok, whatever form it takes. There is no oranges and apples here. At the minute you force on others your religion, you are wrong.
In the past a few cities or public schools have forced the jilbab on their non muslim PNS. The official reasons were "respect", "local culture" and "modesty".
Indonesia is not a Muslim country, Bali is not an Hindu island nor North Sulawesi is a Christian region. Indonesia and its region are a land of several religions who have to coexist without imposing themselves to others.
One can decide to stay home and not go jogging on Nyepi but you certainly shouldn't end up chained because you don't.
Wondering when/if Nyepi falls during the same time than Lebaran. It is something which can definitely happen since none of the date are fixed. Do you think that the Balinese religious police will chain up all muslims celebrating the end of fast? Who's gonna be considered the "Guest"?

In 2024 and 2025 Ramadhan will fall in the same month than Nyepi is. In 2024 Nyepi is deemed to be on March 11th while the start of the Fasting month will be March 10th.