Not taking a position on whether single ship TFs are gamey or not, but whether it happened in the war is only one piece of the "is it gamey" question. The other is how does the game engine handle the activity, and does that produce realistic/historical results. A historical move might be considered gamey if the engine was incapable of producing reasonable results.
For example, if the engine has a bug where if you bomb at very high altitudes you get the accuracy of a very low altitude bombing, but still take flak as if you were high altitude (I seem to recall something like that early on), then it would be gamey to make very high altitude attacks. It may have happened in the war, but the limitations (or in this case bug) of the game engine make it a gamey technique nonetheless.
Yes, if there is a flaw in the game mechanics, taking advantage of it is gamey, however, in some cases the game mechanic "flaw" actually replicates real life difficulties that people are not aware of now (the "flak gap" comes to mind - it existed in reality according to some authors, but to what degree compared to the game is debatable.)
But back to the original question: i don't think the results of single ship "TFs" differed a lot from how the game handles it... if there is sufficient scouting and airpower around, a lot of them get sunk... the game does not replicate the effect of small islands on the difficulty of air power to find and attack ships/boats... many ships and boats used them to successfully evade air attacks in leaving the PI and also Singapore/Malaya. If anything, the game is much more harsh on the single ships in the later case (Singapore/Malaya) than in the game.