The Daily Mail words their claim as follows:
[The yacht skipper Nikki] Henderson's flight from Britain to the US likely produced the same amount of emissions the journey hoped to save, countering Ms Thunberg's mission
This incorrectly characterizes the net CO2 gain of the voyage, because Henderson purchased carbon offsets. Of course, carbon offsets are not a perfect way to combat CO2 emissions; but creating an ideal model trans-Atlantic journey for scalable minimal emissions is not what "the journey hoped to" accomplish and its "mission," and the claim that the end result was "more emissions than the journey hoped to save" is thus false. Nikki Henderson writes on her Facebook page:
There were good reasons to choose someone else - for example, the fact that I had to fly was not ideal considering what the trip represented, even though I did buy carbon offsets. [...]
Whilst it could be misinterpreted this way, this trip was not about telling people what to do, or how to live. It was not about Greta or any of us travelling in the most sustainable way possible. If it was, there were probably slightly better options - although none perfect. There may have been skippers who could have joined the boat in two days without flying. There may have been boats without a diesel engine as a back up for power. There may have been vessels that could monitor their carbon footprint more closely.
This trip was about the bigger mission. It was for us to enable Greta - one of our influencers - our role models - to travel in the way that she felt was most in line with the youth climate movement message: To highlight the need for big structural change to fight the climate emergency. To make the point that there isn’t a sustainable way to travel yet, and there needs to be.
Greta herself made an identical statement.
"I’m not traveling like this because I want everyone to do so, I’m doing this to send a message that it is impossible to live sustainably today & that needs to change. It needs to become much easier."
So, in conclusion, the skipper purchased carbon offsets, but both her and Greta are aware that this form of travel does not scale, and avoided flying in order to send a message that avoiding CO2 emissions is difficult now and needs to become easier.