I guess you are including injury time when you talk about these '5 minute periods' ? In which case the '5 minute period' with the most goals conceded in it actually lasts for 9 minutes or so most matches, so not surprising there's more goals conceded.
Not exactly. All (or most) of the goal times I've used have been from the Ultimate A-League site which incorporates stoppage time into the times so that nothing is over 90 minutes. In other words, they stop the time when there is a stoppage, rather than letting it run like in the game. When compared to other sources, the goal times have mostly been slightly different to ones that include times such as 90+n.