DC-to-DC conversion for solar, off the shelf or custom?
Off-the-shelf products are used when you just want something to do a job, and don't need to know what kind of circuit it uses. If it does the job then it's good. 

If a product doesn't meet its claimed specs then it may be fraudulent, or you don't understand the specs.

Everything is a compromise. You are using Lead-acid batteries - that's a compromise. 

A 12V lead-acid battery isn't 'just' 12V, its voltage may vary from over 14V at full charge down to 11V or lower when discharged. A converter which is optimized for this range may work slightly better than one which is designed to handle higher voltage. Or it might not, depending on the particular circuit and components used in each converter.

Off-the-shelf converters are usually single output because that's what most customers want - and there's no profit in having your shelves filled up with products that people don't want! 

A multi output converter is only good for a specific application that needs a particular combination of output voltages and currents, eg. a PC motherboard. They often have a single switching circuit that uses a transformer to generate the different output voltages. As a result there may be some interaction between outputs. This is a compromise, but works for certain applications.     

Custom Design

If off-the-shelf components are not satisfactory then a custom design is the only solution. But that has its own compromises, so before you decide to go that way consider whether you really need it, what the tradeoffs are, and what difference it will make to the whole system. 

Don't get hung up on converter efficiency without considering other components in the system. Why are you using lead-acid batteries? Why do you need multiple output voltages? How much capacity do you really need, and what are you willing to do to get it? 

Solar systems generally have very poor efficiency because the panels themselves are not efficient - but that doesn't matter so long as you get the power you need. Variation in solar output due to weather conditions is so great that worrying about a bit of extra loss in the converters is pointless. If you are so close to the limit that it makes a difference, you need more capacity!      


  So, what would be a good solution here? If I am trying to get >95%
  efficiency, is cobbling together commercial products "good enough"
  (Option 1) or should I look at a multi-switcher box (Option 2) or go
  whole hog and try to make a custom board (Option 3)?


First drop the requirement for >95% efficiency. Then decide whether the effort of producing a custom board is worth it. Complex switching converter designs are not easy to get right, so unless you have experience in this area it might be better to just use proven commercial products.