Properly used latex condoms which do not break are highly effective for preventing most STDs. They are close 100% effective for prevention of those STDs transmitted across mucosal surfaces like within the vagina or the penile urethra. Those STDs include HIV, gonorrhea, chlamydia, non-gonococcal urethritis (NGU - for men), and trichomonas. On the other hand, for STDs spread through skin to skin contact (syphilis, herpes, HPV), while condoms have been proven to reduce risk for acquisition of infection, they are not 100% effective due the fact that all infected sites might not be covered and have a barrier in place to prevent transmission.
Hope this helps. EWH
In other words, if skin rubs against skin, there is a chance for syphyllis, herpes, or HPV to be potentially spread. Is this common when condoms are used, or a rare occurrence? Also, if you are careful, only use positions where you can visually see the penis penetrate the vagina, and only the condom makes contact, how improved are your chances to ensure none of these STDs are passed?
No, these are not common. Condoms cover the areas where most syphilis, HSV and HPV infections occur.
Your second question is a "what it" suggestion which is probably impossible to accomplish and for which there are no scientific data.
My advice is to choose your partners with due caution and to use condoms consistently and correctly and otehrwise not worry too much. EWH