This has been something that I know I've gone back and forth on a lot in the past. There was a period of time in 2E's development where I had these strictly separated, then merged them back again. It's been a constant battle.The more I work and test this, the better it works to not conflate Explorer and Scout, especially since Explorer is now a Maint-only trait. Fluff wise, Scouts are battlefield electronic warfare ships, Explorers have endurance crews, science labs, and what not. I would suggest sticking with this version and eliminating the use of Scouts for exploring. In this way, a fleet of four Explorer light cruisers (a full maintenance group, costing 3 EP per turn) would only need to roll a 2 or above on their D10 exploration roll to chart a jump lane. Larger ships would give near-sure Exploration successes, but players need to ask whether having them so far on the edges of the empire (or having sky high maintenance costs for every 2) would be worth it.
My biggest personal barrier to removing Scouts from exploration is that in some games like Babylon 5 Wars the Scout/Explorer role is pretty much one and the same, and Scouts there are also used to explore. VBAM still has enough of the B5W DNA in it that it's sometimes hard for me to separate the two.
There's also the issue that then we'd have to give each fleet a unique Explorer unit or force them to rely on a generic Explorer from the universal list rather than using their own Scouts to do the job.
This is a situation where we could have the Explorer-only rule be standard, and then include an optional rule if you want to use Scouts to explore, too.
I agree that the Explorer CC as Scout value equivalent does seem to work well. The reversion to 1E Companion style bonus calculation, while a bit more involved, does moderate the outcome better. Those 4 CL explorers (CC 2) would then get +2 from the first CL and +1 from each of the other 3 (+1 per 2 Scout equivalent) for a total of a +5. That gives them a 50% chance of exploring a lane each turn, which is pretty great odds, and much better than a comparable number of Scouts.