On reading The Origin of Species (ch4)

...but in all cases natural selection will ensure that modifications consequent on other modifications at a different period of life, shall not be in the least degree injurious: for if they became so, they would cause the extinction of the species.

From other sources I know of the way that some genes can piggyback on the success of others just by being close to them on the genome(?). Now, I know that what Darwin said is generally correct, but I cannot see where he would have got that statistic without also noticing that there are also deleterious inherited effects.

Natural selection obviously selects for the benefit of the beneficial gene, and not for the piggybacker's deleterious effect. And should the deleterious effect be worse than the beneficial effect, presumably it would be selected against. And of course it is all relative. When the environment provides a niche that selects for a particular benefit the piggybacker's effects are perhaps neutral....until such time as the environmental forces start selecting over the remit of that sort of effect.

So what am I saying? Just that Darwin wasn't aware of genes and how his theory would get reworded once we understood more about how selection works on genes?

I'm not sure! I'm just dumping my thoughts onto a post; there is no direction to them (yet?). I would like at some point to summarise everything I've written into a post that is more comprehensive, and perhaps actually has a point to make. For now, bear with the ramblings of my mind.