When dealing with multiple drop-ship suppliers, you do have three basic problems you have to be aware of: Shipping costs, shipping times, and warranty returns.
On a multi seller platform like eBay, it's actually easier to deal with than dealing with the problem on your own site. The chances are with a customer on eBay, they are only interested in a particular product, so that's where their focus is, they aren't looking at your other products and comparing things like shipping times and so on.
So this isn't always a big issue on a site like eBay, it's really only an issue if you are cross marketing your products in an effort to increase sales. Then you do have to be careful because you are encouraging buyers to compere those things and having different shipping times, rates and so on, can cause a lot of customer confusion.
How to get around it?
Well you really only have very limited options available. You can either list each product as per the supplier's requirements, meaning that there may well be differences across your range depending on the suppliers you're dealing with. Alternatively, you can create a block tactic, which would be taking the longest shipping time, the most expensive shipping cost and develop your own uniform warranty policy so you have a uniform structure across the board.
That way, if you have suppliers that ship quicker than others, then those customers will get the items quicker than they expect.
I would probably suggest using a block method if you were talking about your own website because uniformity would be very important in that aspect. For a site like eBay, you need every possible advantage you can get, so using a block method can hurt you because you are using a worst case scenario to develop policy and while that will give you uniformity, it can also burn you with buyers.
So for me, you just have to work within the best limitations that each supplier can offer you. If that means one product ships quicker from one supplier, than another for a different supplier, then so be it.