Erabe is imperative but to say suki sounds gentle or less strict than an order like "choose whatever you want" rather than "choose the method you want!"
This doesn't feel like a question but I will answer what I think you are asking, which is maybe:
Is using 好き in an imperative sentence as strict in commanding as in a sentence without it?
To compare what you're describing in the body of your question, it's closer to saying Choose the method you prefer in an imperative way. It is a direct way of saying it.
In order to change what is being said, you can also just say 方法を選べ. This is MUCH more direct and just says Choose a method.
Likewise, if you'd like to be gentler than the original phrase, you could opt for 好きな方法を選んでください, which translates to Please choose the method you prefer, more or less. This is probably the gentler yet formal choice when expressing this request.