Baja's population will be larger as the area around Cabo San Lucas will be developed sooner than OTL...
One by product of this is that the Hispanic/Mexican population of California will be smaller than OTL as there won't be a direct connection between California and Mexico except possibly some really nasty desert between Mexico and Northern Baja (depends of where the lines are).
That would make more sense if the vast majority of Californians of Mexican descent were all from Baja California ancestrally. But they are clearly not; they come from a wide range of Mexico.
Behold this map:
So OTL in order to get to the staging area of northern Baja CA, they must make that allegedly arduous desert passage anyway, across Sonora. Or take a boat from somewhere down the eastern shore of the Sea of Cortez--but the OTL pattern of build-up doesn't suggest that is a major channel to get to Tijuana.
The major corridor appears to be that now represented by Mexican Federal Highway 15, which runs up from Mexico City to the Sea of Cortez coast at Guaymas, pretty much the same latitude as the border between the Mexican state of Baja California Norte and the territory of Baja California Sur; there the road turns pretty much due north to pass through the state capital of Hermosillo and on to Nogales, a dual border town with namesakes in Sonora and Arizona.
Changing the status of Baja California would have no negative impact on the influx of people from Mexico into US California I can envision whatsoever; they didn't drift in from just over the border, they emigrated from points very far away from the border with the goal of working temporarily or settling permanently in the USA, by whatever route they could find. If anything BC as US territory or state merely opens up another channel, albeit not a very capacious one, for entry.