The newer “transformerless” design UPSes tend to be physically smaller and lighter than transformer-based units.
Many of them also tend to be more efficient when operated under partial load (a UPS in a 2n configuration might only run at around 40% of its rated capacity, for example). That said, there are many good UPS systems available, both with and without transformers, so that should not be (IMHO) the determining factor in selection.
In regard to your second question, eliminate the word “transformer” from the question — there are good modular units both with transformers and without. Properly designed, both conventional redundant parallel configuration and modular n+1 configurations give adequate protection. Modular n+1 configurations tend to cost less than redundant parallel configurations.
Remember that the batteries are the part of the UPS system most likely to cause a load-shed failure. Modern UPSes are extremely reliable, but no so their batteries! Whatever the configuration, be sure you have redundant battery strings — redundant parallel configurations have then by definition, as do some brands of modular designs — or better yet, a battery-free design.
I’m sorry my answer isn’t more specific, but with UPS system design, one size doesn’t fit all! There is a lot of FUD being spread by some salespeople. All the major manufacturers have some excellent products, but what might be the best design for a specific data center may not be the best for another.