When I look up guides for champions, I consider them just that: guides. And when I look at the "champions," as you call them, I don't really bat an eyelash. I just understand that his/her runes are reflections of how he/she plays. And most of these templates--especially if you go onto tsm's website--all say runes are preference, just like masteries.
So what I get from that is, master/rune how you play. For me, I main* (that's a joke, but will serve as an example) singed, and guides I've read have told me to get ghost and flash, or to go 0/21/9, but I use my own SSs and masteries that I feel comfortable with.
Not to reveal anything, but I know, as I play, that I'm too aggro and I like to split push... so I grab ghost and tp so I can sustain top better and jump to the bot lane when the enemy just lost a 4v5 at barron (or some random moment that you can't usually predict!)
I also know I'm not amazing with CS, so I'll grab the gold/kill masteries and minion dmg stuff. It sounds like I'm losing out in the end, but I've always found my endgame to be very comparable to my enemies--team fights I do especially well in... I'm not sure why, but I do--and it's the beginning solo lanes that I have trouble with...
So I go flat runes early--def and mag resist, so i can not only sustain against my top counterpart but also venture into the mid and take that AP Mid's dmg while my own AP Mid blasts the S*** out of him/her.
To go on a tangent, if I play sona, I grab gold/5 yellows and quints. Why? I like to play passive/roamer when I support, and I let my AD carry control the bot like he's soloing it. CV/wards (that extra gold really helps) is a killer win for my team, and when my AD (graves or sivir are great examples) is really farmed, especially to the point where the enemy mid Karthas has only 20 more CS than him/her, that's a great situation for the team overall. It puts us on top.
So the moral of the story is, play with what you like. If you like the scaling health/lvl, then go for it. I've personally always found flat runes more efficient (as the game is really won, at least 80% of the time, early game) but as I saw this last few days in the Kings of Europe Tourney, scaling can work quite well if you're patient enough. Just do what feels right.
One last note: don't base everything on the tourneys, either, because that will just disappoint you. You'll find that if you mirror everything these pro gamers do on lower ELO, it doesn't work out as well as you hope. Why? Because people are not at the level of play these players you watch stream/compete are. And everything can change with a reckless player who's paying more attention to when he can gank you in the mid than when the next dragon spawns. I've seen numerous games where my team simply out played the other team in the "meta," but got our asses handed to us in the real game that was occurring. Don't underestimate a damage heavy team, or an aoe heavy team... etc. Adapt, play, win, and pray to God you don't get wasted rank games like most of us do.