No, it is not the same testing and yes, they are comparable when you just want to know about your hablogroups and accept slightly different nomenclature. I would suggest to list them separately to avoid irritations by enthusiasts who start to discuss the pros and cons and ifs and whens.
A bit more detail:
National Geographic has FTDNA doing the testing as they do not have own facilities. Genographic has a different focus on the whole DNA testing. It is not their business proposal to find genetic cousins but to do research in deep ancestry and build public awareness. It is a win-win situation. That's why FTDNA stopped their deep clade program (which is inferior to the specific Geno 2.0 chip) and that's why Geno 2.0 does not provide you with a list of STR values or a autDNA matching for genetic cousins.
The Geno 2.0 test is a single test, while FTDNA provides a broad portfolio of DNA tests to perfectly adapt to the buyer's interest and purse. At FTDNA you pay very little (about $40-50) to get a glimse (or to get you hooked) and pay a lot for detailed DNA analysis. Geno 2.0 is very moderately priced, you contribute to research and indigenous projects, but you just get one set of results and a nice poster to print out.
Geno 2.0 gives you 2 hablogroups (paternal and maternal) beside a regional adjacency of your autDNA and the percentage of DNA you share with neanderthal and denisovan sources. The Y-DNA and mtDNA information goes quite deep into the subclade.
Y-DNA: I did a Y-12 marker test with FTDNA and got a M-269 which is the shorthand for R1b1a2. Via Geno 2.0 I warped down to R-CTS10893= R1b1a2a1a1a*. (As CTS10893 is a quite new SNP to test, there are of course discussions going on, whether it proofs even deeper subclades or not).
mtDNA: Geno 2.0 gave me a pretty good understanding on my mtDNA. But it has just analysed 30 % of the DNA and is a bit of a dead end for deeper analysis.
Update 2013-08-08: I received the result of my FGS which analysis 100% of the mtDNA done by FTDNA: The result U5a1d2a, which was exactly what Geno 2.0 had already given me. Yes, the FGS allows a hunt for new subclades and yes, it is better for searching for cousins. But I paid about $ 200 and the only guy that shares the same haplotyp and extra mutations so far does not answer.
I still need to understand if the Geno 2.0 data after transfered to FTDNA can be used with Gedmatch. I keep you updated.