They are undergraduate Masters - not the same as a post graduate Masters.
As titchy says, this is really not true - they are certified to be level 7, although they are shorter than MSc courses, which run through an entire calendar year.
The main reason MSci/MMath/MEng courses were introduced (20 years ago) was lack of funding for masters in science and engineering. Bachelors degrees are not sufficient for those who want to go into careers related to the sciences/maths they are studying - UK bachelors graduates aren't competitive against graduates from elsewhere in the world, where masters degrees or higher are the norm for highly skilled jobs.
The new funding for postgraduate degrees will not change the necessity for these courses, as undergraduate financing allows for both 9k fees plus maintenance loans while the new postgraduate financing gives only 10k in total. Separate masters in maths and sciences subjects typically cost well over 9k, because of the high costs of running the research project component (plus MSc are 12+ months).
the negative is that you just get the one qualification and it doesnt sound quite as stretching as doing it separately. Also if you do it separately you can choose your specialism.
Both points are not really correct. Employers are perfectly well aware of what MSci qualifications are, and the differences relative to MSc. They know that both are level 7 but the latter are longer courses. And generically there is freedom to switch specialisms within MSci programmes; there is also the freedom to graduate after three years with a BSc if one really wants to an MSc in a completely different area. Separate MSc programmes in sciences can be cash cows aimed at foreign students in specific areas e.g. financial maths.
The only negative about applying for an MSci/MMath/MEng degree is that typically you are asked for one A level grade higher than the corresponding Bachelors. The positive is that indeed you seem more committed to the subject, and may therefore be more likely to get an offer from a selective course. If you start in the Bachelors you can almost always transfer onto the MSci/MMath/MEng programme until the end of the second year, provided that you are maintaining at least a 2:i average.