To be fair to F@H, if memory serves me, their concern was the latency that the BOINC client introduces, namely that a project may be suspended to run another.
Their argument was that since each new WU depends on the results of an earlier one, they needed a quick turn-around time in order to keep the WUs churning.
I guess that one may conclude from such requirements that F@H needs to have the CPU for itself as much time as possible. IOW, it cannot (or doesn't want to) afford multiple projects competing for CPU time as BOINC does.
As far as I'm concerned, it was all a PR wash; or a pleasant way of insisting "you give us all of your CPU time or you get no support". They never wanted to support BOINC, because they didn't like the idea people could run multiple projects. Thing is, in terms of public relations it can be good to put pleasant language to it, and give a face that will make potential volunteers happy. I never did believe they had true intentions of supporting a BOINC client.
And to their stated argument, Milkyway's algorithm is such that new WUs do depend on the state of one's previously turned in. In fact, the results turned in, generate new WU's based on their own blurb on their website for Milky work. Difference is, Milkyway went the route some suggested; just impose short deadlines. Taking away the freedom to crunch multiple projects was never considered a requirement from Milkyway's perspective.
All's fair though. They had chosen to be (IMO selfish) with potential donator's CPU time. In turn, I eventually ended up detaching from/uninstalling folding@home, and chose to not crunch for them anymore, at the requirement of micro-maneaging multiple pieces of software. They can chose to only run a stand alone client for purposes of not permitting potential crunchers a choice of what projects to run along side (perhaps using deadlines to their advantage also). But in consequence, if I'm left with the choice of "give us all of your CPU time, or none" I can chose the latter, and had
True, we're talking CPU time rather then money; but I'd say much the same if one charity made it a condition of contribution that a portion of any potential income can
not be given to another charity, while they recieve donated funds as well, on grounds "well we might not get money as fast to advance our own project". It can be an important cause also, but in the end it would be like "OK, well under those conditions, I'm sure someone else would be happy to recieve said assistance and funds. I never did expect such a condition of "can't give to others also" to be part of the bargain

I really just don't like such conditions or stipulations in giving, when it's mine to chose who to give to, etc... I just never could be very happy when it's put to me like that; when I'm the one being grascious enough to donate in the first place. Sorry but, well there's others who give, so they're OK without me...