Why is research assistantship decoupled from masters/phd program?
This is very difficult to answer authoritatively because each program is different but here are some reasons:


As @Brian Borchers noted, sometimes the admissions and RA funding committees are separate. At some universities, admissions is handled by the department while the RA funding has to be petitioned from the graduate school.
At some places, the lack of funding in the 2+ year is a weeding mechanism. Weaker students aren't offered funding, so they are disappeared (or they pay full fare which is even better than disappearing).
University or department finances may be such that they are not permitted to make a 2 year commitment. They hope that funding will continue but they are being cautious.
They may hope that rather than a university RA position, you will be switched to an external grant funded RA position. They can make a stronger case for funding "unfunded" students this way.
Something else.


The best thing for you to do is to talk to the director of graduate studies AS WELL AS to current graduate students in the program. People on the internet can't tell you which scenario it might be.