First, the definitions, then a slight twist on the statement you posted, then hopefully an illuminating answer.
Cross-Sectional Study: A study where you take a "snapshot" of a population at a single point in time. You're not following anyone, it's simply a "At this point, do you have or not have a disease" - along with covariates of course. A cross-section - hence the name.
Case-Control Study: A study usually used when a cohort study or RCT is going to be difficult, if not impossible. You sample cases from some source, and then a number of controls, usually in some ratio to the number of cases (1:1, 2:1, etc.). Again, you're not following anyone, you're back tracking. Rather than saying "what exposures lead to disease" you're asking "what exposures are more common in the group that got disease?".
What the statement means is that in either case, you're limited to what you can estimate. In order to calculate a risk (and thus a risk ratio) you need to know of a population n with no diseased people, how many people would get disease in your follow-up period (incidence). In a cross-sectional study, you technically only have prevalence, not incidence. This is the twist - the statement you posted is technically wrong. You can also - and often should - estimate a Prevalence Ratio from a cross-section study, as well as an Odds Ratio.
In a case-control study, you don't have the population - you just have the cases, and a basket of non-cases - you have no idea what happened in population n. So while you can calculate odds, its literally impossible to calculate the risk, it requires information you do not have.
However, in cases where disease is rare (~<10% prevalence), the Odds Ratio should approximate the risk ratio for a similarly conducted cohort study.
What this all means statistically is that these relatively simplistic (and thus fairly flexible) study designs are somewhat restrictive in what you can do - you're largely confined to logistic regression and the calculation of an odds ratio.
I don't know which p-values are appropriate in your case since I do not know what your data is like. For the Pc1df p-values I do not know what "corrected for possible inflation" means (population stratificaion perhaps?)
P1df: corresponding list of P-values of 1-d.f. (additive or allelic) test for association bestween SNP and trait
P2df: corresponding list of P-values of 2-d.f. (genotypic) test for association bestween SNP and trait
Pc1df:P-values from the 1-d.f. test for association bestween SNP and trait; the statistics is corrected for possible inflation
source: http://www.genabel.org/GenABEL/scan.gwaa-class.html
Best Answer
Logistic regression is a valid inferential method, because, as you've noted you're modeling the odds. The coefficients on explanatory variables $X$ will also be valid. However, the intercept term $\beta_0$ will not be; this is because the number of positive and negative outcomes are fixed by the case-control design. So the intercept term will be meaningless, but your other estimates are fine. More information is in Agresti, An Introduction to Categorical Data Analysis (second edition; 2007), p. 105.