The gemara explains that the braisa that considers grabbing the stringent opinions to be foolish - כסיל בחשך הולך, only applies when there is an inherent contradiction between them. The example given is the halachos of tu'mah and treifa that result from the machlokes whether a spine missing a vertebrae is considered complete. The opinion who considers it complete is a stringency of tu'mah but a leniency of treifa, the opinion who considers it incomplete is a stringency of treifa and a leniency of tu'mah. To be lenient in both would be a רשע and to be strict in both would be a fool. Although the gemara says that R. Akiva was machmir for both opinions regarding when the new year begins for ma'aser, that is because he was trying to follow Beis Hillel, just he wasn't sure what B"H held.
Perhaps a practical example of this would be the famous argument between R. Chaim Na'eh and the Chazon Ish regarding shiurei torah. The CI was notorious for having large shiurim, whereas RCN has smaller shiurim. In the context of creating a wall, the CI would be the stringent opinion, but in the context of a breach in the wall the CI would be the lenient opinion by holding of a very large amah. An eiruv that is constructed based on the shiurim of the CI for walls and machmir for RCN by breaches would seemingly be a prime example of כסיל בחשך הולך. It would seem that this is even worse than the case of the gemara. In the case of the gemara, at the time he is being machmir by treifa, he isn't being machmir by tu'mah, and days or weeks later when he is machmir by tu'mah he isn't being machmir by treifa, so that each even independently is acceptable. Yet, the gemara considers him to be a כסיל בחשך הולך. Certainly in a circumstance where the entire eiruv is built on the two stringent opinions being used simultaneously, it would be considered a כסיל בחשך הולך.
One of the members of our kollel suggested that the case of an eiruv might be different because it is being built to be used by a community. Although for an individual to be machmir for both opinions and certainly to construct an eiruv based on both opinions, would be a foolish practice, but a community may be different. Within the community there are those who hold like RCN and those who hold like the CI, therefore it would seem acceptable to construct an eiruv so that both those who hold like RCN and those who hold like the CI are able to carry. However, someone else pointed out that the case in the gemara where they were machmir by the mavuy akum for both rav and shmuel was also a case of a public eiruv for a mavuy, yet the implication is that only because there isn't an inherent contradiction between the two opinions was it acceptable. The gemara implies that had the opinion of Rav been an inherent contradiction to Shmuel, the eiruv would not have been constructed in that way. But in truth, there is no proof from the gemara. In the case of the gemara, had there been a contradiction between the opinions, it would not be possible for one to hold that the bent part needs to be fixed and say that it needs a door. Therefore, those who hold like Rav would hold that it doesn't need a door (just a tzuras hapesach) and those who hold like shmuel would hold that it doesn't need anything.
It seems to me that the entire concept of כסיל בחשך הולך only applies when one is trying to be machmir for both of the two opinions. However, if one would have their own halachic opinion, but be unsure as to the precise size of an amah thereby leading to a gray area in which they need to be machmir, that would no qualify as a כסיל בחשך הולך. For example, if one would be machmir for the opinion who says כדי אכילת פרס is 3 minutes for matzah, but on Y.K. be machmir for the opinion who says 9 minutes, he would be a fool. But if the reason he is machmir is because he himself is me'supak about the shiur and the entire span from 3 to 9 minutes is a safeik to him, he would be entitled to be machmir and not be considered a fool.