Actually, recently with my latest extraction using the manske tek/tao of rue, just tried using the whole seeds. I went ahead and did multiple 'boils' of the seeds, more than reccomended, 4x if i remember. So there was a lot of liquid to filter and further reduce. However, my yield didn't seem to be as good; around 10g, but I had used a slightly larger amount of seeds to begin with than i normally use to get this amount... So while 'most' of the alkaloids may be on the outside of the seeds, it seems like there is still a significant portion on the inside.
Also, since I had such a large volume of liquid that was reduced, my resulting crystals were quite reddish. I basically stopped after the second manske but I have had other extractions that produced yellow(er) crystals as soon as the first manske was done. Not sure what exactly the red color means , maybe it's even a good thing. I do plan to redissolve and basify at a later point but I remember expecting a bigger yield given how much rue I used and how much I had boiled the (whole) seeds. For sure the filtering is way easier. However, maybe in the process of the extreme filtering with using ground seeds, some more of the impurities are taken out before even getting to the manske-ing?
I think if you have the time and patience and materials it is better to grind the seeds from my experience, but maybe the 'payoff' isn't worth it because you'll be using way more filter papers/cotton balls/coffee filters and for most people rue seems to be relatively inexpensive. Not to mention the time invested in said filtering.
The tao of rue also says to collect the filters/cotton balls etc and do another acid extraction on them, but I found that my yield from doing this extra work was minimal. As well It seems like all the sludge/dust sitting in the filters once again was a total pain to filter out after boiling them so for me I haven't seen much incentive in saving the filters/cotton balls. I wish I had taken a picture of my crazy collection though after doing one complete tao of rue, it seemed a bit excessive how much filter media it took. Of course with the ground seeds, less so with the whole seeds.
Also since I am using so many cotton balls I opted for organic cotton. I used to think organic cotton cloth was for 'crazy people' but looked into it and I guess cotton is one of the most heavily sprayed with pesticides crops there is. Maybe something to consider for those doing the tao of rue.