I wouldn't trust spot putty to be durable in the long run, it won't flex as much as the plastic, esp in the temperature fluctuations of a car.
A much better alternative would be a 2-part high build primer like this, it's basically sprayable body filler
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If you don't have spray equipment you could easily use a polyester glazing putty, something like evercoat poly flex which is made for adhesion to plastic and is semi-flexible. I don't trust non-catalyzed products to be durable.