You could just split and then mothball part of trade fleet so it won't auto merge but I would say it is silly to risk your trade fleet if you are fighting a superior naval power anyway.
So it never occurs that a superior naval power suddenly declares war on you while your trade fleet is at sea. Or do you just never have any ships at sea on the off chance you get ambushed?
The counter argument included the suggestion that If trading in the Mediterranean you add galleys to your trade fleet rather than heavy ships, the suggestion to add heavy ships was mainly for trading outside of inland seas. Also, people pointed out that splitting your fleet does not make it any less vulnerable than having it in one group unless you are really good at micro, in many cases it makes it more vulnerable.
I'm sorry but as I pointed out if you have 6 light ships having 2 galleys and 4 lightships instead would be pointless, not only would they not be a deterrant but their upkeep would eat into your trade income making having a trade fleet pointless anyway.
None of these are arguments for not making it optional. As I've stated I think merging trade fleets is a desirable improvement but don't tell me it's not at the cost of some gaming freedom if it isn't made optional because you'd be wrong. You can't argue that on any level.