No it isn't too late. Just send a LOE from webform. There is no specific format and it doesn't have to be an essay. Just 5-6 lines are fine. No one has time to read pages of LOE.Thanks for the prompt reply @cansha! The application status on very first page is "In Progress". Hopefully, there is still time to submit an LOE with clarification. Any specific format to follow or anything to keep in mind while submitting LOE?
With regards to work experience and FSW score, I am good.
Thanks again!
In any case, personally I would be extremely surprised if your case is refused because of this. It is a mistake but a TRV refusal shouldn't lead to a PR application refusal. However, only issue is if a visa officer is being really strict he can argue you hid visa refusal information on your application. But that is too much speculation for now. Only thing in your hands right now is to send in a LOE and explain why TRV was refused and why you hadn't sent passport for original TRV application and hope for the best!