I infer you mean you have a stained hardwood door, and I guess it will be panelled.
You can use wood dyes such as Ronson's to colour the bar to be a near match to the timber of your door, before you apply the protective stain. Stains are usually tinted, so will make it darker, and probably redder or browner. Staining the door and the bar before you put them together will ensure that hidden parts are protected. Letting it harden will prevent them sticking so much. It is easier to sand and repaint a door in future if you take all the hardware and bars off.
The reason for buying brass screws about 60mm long:
the door will be 44mm thick. This will allow 16mm to stick through the outside of the door. Position these so they go into the bar at a point where it is thicker, and the points will not come through. The bar is roughly triangular in section, and about 50mm at its thickest. the screws should be in the top half of the bar. If you use 50mm screws they will only penetrate by 6mm which is not really enough, unless you countersink the heads deeply inside the house. With brass screws you can nip the points off to shorten them if necessary, but it is essential to drill a pilot hole in the bar first, as brass screws are weak and break easily. Only use one row of screws along the bar, if you use two rows, or stagger them, it will crack in dry weather.
edited:
if the door is not well hung, you may do better to find a skilled local joiner, who will do a better job, quicker, than an amateur. Hardwood doors are heavy, but a semi-retired man can do this sort of job easily enough as he will have special folding wedges to hold it up. Skill and care are important in getting a perfect fit to a door. I am not a professional and find it quite hard (my front door weighs 41 kg plus the glass and hardware) so I plan to ask my local joiner to re-hang it on lift-off hinges one day.
BTW most hardwood weatherbars will be in a sort of "mahogany" substitute, a reddish wood.