It's a rule of thumb, as you say.
I'd put it whimsically: the intercept doesn't know it's different, so its estimates feel free to misbehave. So yes, the intercept is included. Even more so, the intercept doesn't know if you don't care about it or regard it as uninteresting.
I'd turn it round and ask for more information on your concerns. One thing I've often seen is people estimating an intercept that is far outside the data when re-parameterisation would give a better view. For example, people fit regressions to recent data with time in years as the predictor. Hence the intercept is the level at year 0 and is rarely well determined in that situation. Recasting the model to predicting from (year - 2000), or whatever, means that the intercept is the level at year 2000. It's more interesting and its uncertainty will look more sensible.
Naturally, this may be a long way from what you are doing, but the definition of intercept is more a matter of convention than people often realise.