To be fair, it works fine for players to. When I play a colonization game I always go to Siberia to cut off Russia (unless I'm in northern Europe and can just fight them to cough up Perm instead). I agree that colonization is too quick as it is, but if this weren't possible Russia would swarm all of Siberia in record time with no opposition. You'd have to nerf Russia's expansion rate east as well before you start tinkering with anything else.
If you go for exploration right away and start colonies and then withdraw the colonist to start new ones, you can make it to Kamchatka well before the Spaniards can get there. One key thing is don't worry about filling in colonies around your line toward the East. Focus your active colonists always in pushing. In fact, I've found that you only need 1 until you get to the eastern coastline. Then you need to go both north and south to block the western powers out completely. It didn't seem hard to block them out completely to me anyway. It's just a matter of starting the race for colonization early or not. Also remember that you do need the conquistadors since colonists alone won't disclose connecting lands until many ideas later in the game.
On the other hand, having those last few eastern provinces really boils down to what you want to accomplish overall. Spain or even England or Portugal getting a chunk of the Eastern colonies hasn't seemed like a big deal depending upon my goals (I have only seen Castille/Spain show up in 1.7, not sure why).
One approach is to pick up expansion and also Westernize. The reason I sometimes westernize is that then you can very easily grab up all of Ming as a protectorate very easily. They seem to accept protectorate status around 70-75% warscore with low war enthusiasm. Once you take them out, if you have grabbed up Oirat and colonized a wall to in front of the Spaniards, pretty much they cannot really do anything about it, or so it seems. After this or around this time I grab trade ideas because putting traders into the 2 Ming nodes provided me around +30 gold a month as I recall and growing over time.
I am confident this is a fairly easy strategy because I just finished doing this as Sweden/Scandanavia and having enough gold from trade and production to field a 250k army backed by >500k manpower.
So, as with various other aspects in the game, this sort of issue of Spain coming in from the east is perhaps best handled by early strategy decisions. If, for instance, your goal is to cut a swath to the HRE, vassalize electors and become the Emperor, for instance, expansion to eastern colonies with their low tax rates and values, albeit a lot of manpower, is potentially secondary.
So I feel the key is to decide early on what you want to achieve and this line of thinking may naturally take you to preparing for future challenges you will then face in a more prepared way.
