I can't build colonizers fast enough for that to work effectively -- essentially, I'm trying to not have my colonies too spread out because I don't want my empire to be cut off from another part of my empire (ores, and so on, cannot be exploited by planets that are cut off from them -- you need a contiguous chain of planets). Each colonizer that I send to explore would mean one less nearby system I'm colonizing early in the game. Do you actually forgo colonizing in order to explore with that colonizer? And I would probably have to scrap my starting scout as well, because the bonuses are largely being triggered by the scout, and that scout pretty much has explored my frontiers before I can build my second colonizer. I think that the loss of getting that second or third system so late in the game because you decided to explore, would far offset any bonus you might recevieve by using the colonizer ship as a scout.
One other issue I should mention -- colonizer ships are expensive to maintain -- you DEFINITELY want them to be used as son as possible. They do not make good scouts for that reason alone.
I do tend to explore with colonizers the first... 5-6 planets? by then I hope to have at least half of them colonized and my home planet be sufficiently developed to build a few warships and then explore deeper with those.
Technically, I do also, but only because I so rarely find a colonizable planet on my first try. I don't explore with a colony shop on purpose, but that's how it simply works out most of the time.
Also I gotta say the UI additions are fantastic, I love the little "current building" icon and the marker that shows how many ships you have in your hangar.
Ok maybe you play in different settings than I do: huge galaxy, few constellations. Get N-Way fusion first, buy them instantly on each planet you grab (if you have the money: if you haven't just wait till the price comes down so you can: the speed bonus helps a lot in the early game!). Build the farm exploit for 4 turns and then wait till you have a second pop so you can build a colonizer. Basically after turn 30 or so I can build a colonizer every 3-4 turns in my home system. That's a LOT of colonizers. Do not worry about not having all system linked up: you will lose out on too many awesome systems and planets if you do that. It might take too long to research lava colonization or even gas giant colonization for that one system that's between you and a dust Wonder Huge Jungle with 2 prot-orchids. In fact, I find that colonizing far and and then guarding (but not necessarily attacking ships that are stuck) them works well to set a far off perimeter, and then slowly fill up the gaps with empire. It stops enemies from getting too close and colonizing systems of their own. Chances are by the time you're connected you also have researched the stuff that you need the connections for. Also, I find that special resources are often not necessary to have them everywhere. I didn't know they cost significantly more than scouts to upkeep, but haven't had any money issues yet. I literally never made any scout. If I need I insta-buy a few protectors or so, but usually my first corvette/giga (larger hull) is about ready by the time the other empires might be thinking about becoming hostile.