The last 4 listed...Herpes, Syphilus, Chancroid, and HPV are listed as low effectivenes because they produce sores, rather than JUST being a fluid discharged.
If you have a wart or a herpes sore on your penis, and you wear a condom over it, the disease will not be transmitted through the condom. However, most genital sores appear on other genital areas that are NOT covered by a condom. The disease can be spread by simply rubbing up against the sore or the infected area. Herpes is particularly sneaky, because the person with the disease may not have an active sore, but may still be 'shedding' skin cells that contain the virus from the infected area .
The good news is; these 4 diseases are easier to treat if found, being not as life threatening as HIV. Basic recommendation: Use the condom whenever with a new partner!