I wouldn't have thought that the standard checks would reveal an STI unless you had outward signs, (eg Herpes).
The urine test may show up leucocytes, which I have been seen linked to chlamydia, but I'm not sure what urine sticks they use for CAA medical. The last medical I had (class2), urinalysis consisted of only glucose and protein, so would be unlikely to reveal an sti.
I admire your responsible attitude (a condom perhaps would have been even more responsible, but who am I to judge
You should be able to seperate out both consults, as far as I know, sti checks are performed anonymously in the UK. I would have thought that this would be the best option.
You may be better for a response from Obs Graham, he seems knowledgeable in this sort of stuff.