If you connect directly to the battery then the BMW electronics will not affect the charging. As JJH states, a poor quality charger can have a detrimental effect on the battery (or electronics if the battery remains connected to the bike).
Like JJH, I have left a bike with a modern battery, usually an AGM type, for several weeks. Unless there is a drain of some sort like an alarm system then these batteries do not discharge very quickly compared to older, wet batteries.
Like JJH, I would not use a charger unless it is a device approved to the relevant CE regulations from a recognised maker such as Optimate, CTek etc.