What you are doing is converting a timestamp (the number of seconds after midnight 1st of January 1970 in the UTC timezone) to a datetime, and then you format it using the settings provided.
So you are saying I want the time in the H:M:S format of 1st of January 1970 00:35:49 UTC.
However, by default timestamp_custom will convert this to your local timezone which apparantly is +1
So it will give you the time in H:M:S of 1st of January 1970 01:35:49 GMT +1.
To disable this conversion to local time, you need to add false to the timestamp_custom filter.
{{states('sensor.anova_precision_cooker_cook_time_remaining') | int(0) | timestamp_custom('%H:%M:%S', false) }} will give you the expected result.