As mentioned, a lot depends on your goal. Is the goal to be able to see/read something and just get the gist of it or is the goal to speak correctly and be understood by Japanese speaking persons. Incorrect choice of transitive vs. intransitive is certainly one area where what I say confuses and perplexes those I interact with. At home my wife will quickly realize my mistake and correct me (often after laughing about what I said having conjured up an amusing mental image - i.e. me with my face planted on the copy machine at the Family Mart trying to clone myself).
As mentioned, I do agree that when reading you can often quite easily understand which it is from context. The trick comes when going in the opposite direction and speaking. Then you have to choose the correct one without the aid of seeing it context. For me that can often been a quick mental coin toss and hoping I get the right one. I know it is either A or B, I just don’t remember which one is the right one.