They will not look the same because they are different materials.
Do you have a piece of scrap material from the first set of stairs to try this method on first (of applying that mixed second coat?)

Sue, from Nova Scotia....
I too am from there was on East coast near Digby. Am US citizen for many years, live in Florida now.

Varathane is a brand name, but they do make a polyurethane varnish. Is this what you used?

Often veneer and solids will take stain differently. This may be what you are experiencing. Also different pieces of wood, and differently prepared (e.g., sanded) pieces of wood can take stain differently.

The good news is that you can use the gel stain (if that is truly what you have) as a glaze. Add a tablespoon of mineral spirits per quart of stain to slow down the flash off time and give yourself some open working time. Let this dry at least overnight. Then apply another coat of polyurethane. I would test this out on some scrap first, before attempting on your whole flight of stairs. Easier to avoid a problem than to fix one

bob..no I don't think its really varathane..its by minwax and says its a 'oil modified water based polyurethans"...I took 2 small dishes and mixed the gel stain (which is varathane based product by flecto) with both the poly and the varathane...the gel stain would not mix with the poly but it would with the varathane. I currently have 3 test boards going...one with just the gel rubbed on (i am thinking that the next layer of poly will just lift the stain layer)..one with the combo varathane and gel and one with the combo rubbed on over just gel. it seems to be working in both cases but I didn't want to do something that may end up a big mess in 2 months time.
Big Hi Mary...Love Love Love Florida..was there in June for the 3rd time..My son (14) will only get on a plane if it lands in Orlando lol.

I don't blame him! Orlando is like no place else! We love it too! We live about one hour drive South if driving to Orlando.

It is amazing around here from like this month right through to March, this is OUR paradise time (weather-wise!)

I haven't been home (Nova Scotia) for some time now, everything up there has changed so much and cousins all left for Alberta for work. I am so due for a home visit!

oil-modified blah blah blah is really misleading. It's a water-borne finish. This is quite different, chemically, from both an oil-based stain and an oil-based varnish (poly). They won't mix and will be an real disaster if you try.

Water-borne finishes are mostly acrylic, with water as a carrier and gycol ethers as a "softener" that makes the finish work. They are emulsified with a number of different chemicals in a fine balance. Dumping in resin-based vernishes, thinned with a lot of mineral spirits is just "mixing oil and water."

bob...remember dumb blonde here....so does that mean I can put the poly over the varathane and visa versa and either over the stain? And ignore the 'oil modified' part even though the stain would not mix with the poly?