I have never noticed cidery flavors from bottling. The < 5 oz of sugar is not enough to be noticeable in a batch. The only flavors I have noticed that are contributed by bottling would be due to stirring up more yeast due to transporting.
As for kegs, you can get off flavors from them as well.
I keg for convenience. It is far easier for me to clean and sanitize one keg and the autosiphon than it is to do 2 cases of bottles, a bottling bucket, the bottling wand, autosiphon, tubing, caps...
This right here is what bothers me about the pro-kegging crowd. I keg all my beers and will bottle the occasional batch. But I don't think kegging is neither easier nor quicker. Yes, it's quicker to get the beer INTO the keg than into 50 bottles. However, using one of those bottle tree squirter dealiers for bottles makes life WAY easier.
Also, if you do a good job of rinsing out each bottle after you pour one, all you really have to do when you're ready to fill them again is sanitize them. I sanitize the bottles while the priming sugar is boiling, it really takes on a few minutes with a bottle tree and sulfiter dealie.
So, if you factor in cleaning your beer lines, your kegs, etc, unless you're lazy and don't keep your sh*t clean, it takes as long or longer than bottling.
Lately, when bottling, I've taken to a hybrid approach where I'll use a keg as a bottling "bucket" and push the beer into bottles with co2 through a picnic tap with a wand attached to it. Works really well. Plus I can seal the keg and roll it around to evenly distribute the priming solution.
Anyway, if you do it right, bottling can be really easy, easier and cheaper than kegging. I'd bottle, but I've got all the sh*t already for kegging, plus a sweet collar that my stepdad built for me for my chest freezer. So, it doesn't make a lot of sense for me to go back at this point.
Besides, having kegged beer is nice as you can pour any amount at anytime you want. I probably drink way more than I would if it were in bottles.
But, nobody should be knocking bottled beer. There's no reason it should be any different than kegged beer and it sounds like those homebrew shop dudes don't know what the hell they're talking about.
I took a sample of my beer once to a brewery for the brewer and staff to try and I said it was an extract batch, just felt like doing an extract beer, and one of them said, "Oh, that's what that is..." What? You're kidding me dude. This was a hefe and it tasted great. Whatever, dude. Some people don't know WTF they're talking about.