Losing in thought and autopilot kicked in
Is it really a mistake to be lost in thought?


When Satti is absent you create fabrications hence future misery. Therefore, it is a "mistake" to be lost in thought.


  Is my way of countering have bad effect?


You are doing Kayanupassana hence this is one of the solution is being mindful, i.e., mindfulness of the body. In addition be mindful of the bodily sensation when moving like the fabrics touching your body, the wind sweeping over your skin, etc. Also look at muscular pains and pain and pleasure in changing postures.

Ultimately what you have to work with is to realise 4 Noble Truths and Dependent Origination this you can realise through any experience you perceive as good, bad and neutral and this leads to sensation which are pleasant, unpleasant and neutral and even the pleasant and neutral are unsatisfactory due to 3 Characteristics while unpleasant is unsatisfactory on its own and neutral opens us for further existence and it can still give unpleasantness in the future.