In regards to your first point I would point out that any time you bottle condition you will have sediment on the bottom of the bottles, the yeast eat the sugar and produce the CO2 that carbonates your beer. If you filter out the yeast before bottling you will not have carbonated beer. Unless you keg and force carb, but that is another thing altogether.
If you pour the beer slowly and stop when the yeast starts to come out (pouring to the shoulder) you will only leave about 1/4" of beer behind, not that great a loss.
And just like in bulk aging, the longer your beer sits in the bottle, the tighter the yeast cake will get.
Which brings me to your second point regarding the secondary. It sounds like you are referring to yeast autolysis, this has been determined to be not much of an issue by many of the heavy hitters in the home brewing community, including Palmer, Papazian, and Jamial, if you search the forum you will find extensive threads on this topic. But in a nut shell autolysis is a concern for commercial brewers because their fermentation conditions are some what different from that of a home brewer, greater pressures on the yeast, higher temps in the yeast cake, etc...
Plenty of people leave their beer in the primary for months and report no problems, quite the opposite, they say it's some of the best beer they have made.
I would like to try leaving a beer in primary for 3 months to see what happens, but I drink it too damn fast!
Seriously, do some forum searches for threads like primary/secondary, long primary vs secondary or something along those lines. Or look for Revvy's posts and blogs, he has written a lot on this topic here.
The best way to find out for yourself is to try it both ways and see I guess, but I really like the long primary, I don't risk interrupting my fermentation, oxidizing my beer, contaminating it with an extra process step, and (most importantly) I am inherently LAZY and it is so much easier to just leave it.
If you want clarity, cold crash after a 4 week primary, you'll be able to read through it!
If clarity is not so important to you, don't cold crash and you can still read through it! Although you might have some chill haze until it warms up a little...
I think your yeast handling was fine, but many of the dry ale and lager yeasts don't even require rehydration. I usually dry pitch my safale yeasts and they haven't let me down yet.:rockin: Wine yeasts are different and can require rehydration and nutrients to minimize lag time.
My 2 cents