As mentioned earlier, most chemical methods rely on letting treated water contact the threads by holding it upside down and loosening the cap a bit. This is done EARLY in the treatment - not at the end.

You won't have to worry about water on bottle threads with most filters since they pump straight into the bottle from an input tube that typically sits in the source water.

When using the basecamp filters - where you pour water in the top and let gravity move the water down through the filter - people often use collapsible buckets or "dirty bottles" to fetch the water, but drink out of dedicated bottles (including collapsible bladders). This is what Ironraven's recommendation is.

I'm not sure how the UV wand users deal with potentially contaminated water on the outside lip of the bottle - unless one is just very careful to pour the water in the bottle without getting any on the outside lip/threads - a funnel might hep.

I've used both chemicals (tablets & MIOX) and a filter (Hiker). No real preferences either way. They both work.