For bottling, I transfer from the secondary carboy to a bottling bucket before adding Sugar syrup or AJ for carbonation. I leave the last 1/2 inch or so (trub plus a bit of clear cider) in the bottom of the carboy and don't have any trouble with clarity or carbonation. There should be plenty of suspended yeast in the transferred cider.
If I am bottling early (say at 1.005 to 1.010 or higher) for carbonation or for pasteurising to retain sweetness, I will simply bottle straight from the carboy and also leave the last 1/2 inch behind. This costs me about a half bottle (i.e. a 5 litre carboy should yield 15 x 333ml bottles but I only get 14 and a bit) so I drink the bit for "quality control" and as a reward for my efforts!!!
I do sometimes get a very fine film of expired yeast etc on the bottom of the bottle but if this mixes with the cider when pouring or through vocano type carbonation, you don't notice it (or you can pour carefully and leave the last few drops).
In any case it is quite hard to filter out yeast. I understand that you need something like a 0.5 micron filter for yeast (Lea suggests that some big commercial operators use 0.2 microns and I know that one of the local semi-commercial craft cidermakers uses a one micron filter under pressure). One of the smallest filters readily available to us amateurs is a coffee filter at around 20 microns and if you ever try filtering a gallon of cider through that, you will wait for a long time and probably still retain a lot of yeast.
So, I guess the short answer is "don't worry too much about it", just minimise the amount of muck that you transfer to the bottles either through filtering (I sometimes use a double layer of cheesecloth or muslin if there is suspended pulp) or careful siphoning.