I understand that Safek brachos lehakel might simply be a corollary of Safek D'rabana L'kulah, however I assume there is some nafka minah between the two. The only reason we would have safek brachos lehakel is to teach us something that we may otherwise not have known had we only had the rule of Safek D'rabanan L'kulah. My question is: what hava amina might we have had if we only knew Safek D'rabanan L'kulah, that we needed Safek Brachos Lehakel to teach us otherwise?
By brachos we have a couple different issues which need to be balanced. There's the obligation of making the right bracha before eating, the prohibition of eating without a bracha, and the prohibition of making a wrong bracha (using Hashem's name in vain.)
The gemara Brachos daf 12a discusses the case of a person who takes a cup of beer and mistakenly thinks that it's wine. He starts to make the bracha "baruch ata…" planning on concluding the bracha "borei pri hagefen", but after saying "haolam" realizes that it's beer and concludes "shehakol." (I'm avoiding the machlokes in the pshat gemara since it's not relevant for this question.)
Tosfos d.h. "lo" points out that the gemara doesn't clearly render a ruling in this case. He quotes the Rif ruling "leniently" that even in this case you fulfill your obligation. Then he quotes the Ri who rules "stringently" that you need to make the blessing again (i.e the stringency is that you did not fulfill your obligation.)
In the gilyon Hashas there R' Akiva Eiger brings the question of the Magen Avraham- how can you rule "lechumra" the general rule is "Safek Brachos Lekulah?
He answers the question by using the concept of the Maharsha in pesachim: we only say safek brachos lekulah regarding a safek birchas hamitzvah. Since we poskim that birkas hamitzvah is not meakev (meaning that even if you don't make the bracha before doing the mitzvah, you still fulfill your obligation of the mitzvah) therefore when in doubt don't make the bracha.
However, regarding birchos hanehenin (brachos before enjoying something like food) we have another rule: you're not allowed to eat without making a bracha (asur lehanos ba'olam hazeh bli bracha.) Therefore the Ri holds that you need to be machmir on that prohibition (of not eating without a bracha) and therefore make a new bracha. (Rak"a says it's not a chashash bracha levatala since you can't eat without making the bracha.)
Rak"a on that spot refers to what he wrote on Tosfos daf 49b. There, the Ri says to be "machmir" and make a borei nefashos on a drink which is less than a kezayis. Rak"a there asks- how can you be machmir, the rule is safek brachos lehakel? Since on the bracha achrona there's no problem of eating without a prior bracha, we revert back to the general rule of safek brachos lekula.
From the machlokes between the rif and the ri (As explained by Rak"a) we see the rule of safek brachos lehakel isn't a simple ruling based on safek derabanan lehakel.
There's an additional aspect of safek brachos lehakel- when you don't know what the bracha is, you need to make the more general bracha. i.e. if you're not sure if it's a fruit or a vegetable, make a ha'adama. See here for a discussion of the sources.
When I make the ha'adama instead of the ha'etz, out of doubt, what is the leniency? Here, the leniency is on making the proper bracha. If the bracha should have been haetz, and I made ha'adama, I have been lenient regarding my chiyuv to make the better (more specific) bracha.
But I have to be lenient about that, since if I err the other way- I make haetz when it should have been ha'adama- I'm saying sheker and the bracha doesn't count. Thus it ends up that I'm not making any bracha, and I'm eating without a bracha!
Here, we see again that this discussion of safek brachos lehakel is not necessarily related to the question of safek derabanan lehakel.
When the gemara states (35a) that it's forbidden to eat without making a bracha first, it's not clear that it has the status of a torah prohibition. But yet we see that we use the principle of safek brachos lehakel even when we're considering various rabbinic obligations and prohibitions.
[worthy of mentioning- Some poskim, including Rav Shternbuch in Shu"t teshuvos v'hanhagos (I think chelek beis) explain that the issur of benefiting without making a bracha doesn't require an actual halachic bracha. Thus, he rules that if a person isn't sure if he needs to make a bracha (maybe he already made a bracha, maybe he didn't) that he should think the bracha in his mind. While it doesn't fulfill the chiyuv of making a bracha, it does remove the issur of eating without one. Thus on the bracha itself we can revert to the regular rule of safek brachos lehakel.
This is again an example of how various aspects of hilchos brachos come together, and it's not enough to simply say safek derabanan lekulah.]
Penei Yehoshua to Berachot 12a writes:
הא דקיי"ל בעלמא ספיקא דרבנן לקולא לאו כלל גמור הוא דהא בכמה דוכתי פוסק הש"ס לחומרא אף בדרבנן היכי דאיכא טעמא
That which we rule in general that sefeika derabbanan lekula is not an absolute principle, as there are many places where the Talmud rules stringently even in a derabbanan, where there is reason to do so.
He goes on to note that there may be specific reasons why one would think to rule stringently in certain cases of doubtful berachot (and, in fact, Ri does rule that way).
Thus the principle of safek berachot lehakel could be telling us that we do indeed apply sefeika derabbanan lekula in cases of berachot.