Millipore bottle top filters are polystyrene housed, which is not compatible with benzyl alcohol. So if you’re filtering a lot of oil the polystyrene housing will be dissolved into your solution. There are threads here on meso about this. Melted plastic in your gear is not good. You’re gonna want to use glass, or polypropylene if you don’t want any reaction with your solvents and the housing of the filter. It will be very difficult to find pre-sterilized polypropylene housed filters that have the proper membrane filters you need, so you may have to resort to glass, or just try the millipore and use less solvents in hopes the housing won’t leach into your gear. The best option would be to buy a glass filtration system and paper filter membranes. PVDF.
As for transferring the finished product into sterile vials, it’s best to do under a Laminar Flow Hood, with proper clothing on (gloves, clean, long sleeved hazmat suit) which will help prevent any floaters or hair from entering vials. If you don’t have a flow hood and don’t want to invest in one or make one, I would use a bottle top dispenser. It will screw onto the gl45 cap and from there you can dispense into the vials. As long as you’re working in a clean environment and everything is sterile you’ll be fine