Run your throw bar up from underneath

I would just use the holes on either side just like you would if you were using a hole in the middle.  Personally, I’d just put a piece of paper with a slit in it under the ties and maybe hide the works with a scale switch stand.

These are printed in 3D by F&M Models. I’m told they’re available in N and TT as well.  You can see the rod coming up here on this one.

Alternatively, maybe a hole can be drilled in the middle of the throw bar. I couldn’t find good pictures of one of these turnouts.

Thanks

Thanks Mike for the suggestions. Do you have a URL for the company that made those switch stands for n-scale? By any chance anything low profile for sidings?

Thanks!

Nathan

Center of track or side?

 Seems like you'd have the same size hole to cover either way?  I used Atlas code 55 turnouts on my previous N scale layout and don't recall any problem installing Blue point controlers on them. It's been a few years so can't recall exactly how I did it but I likely used the side holes if they came that way. I do recall they had extended ties on both sides so one could cut off the side they didn't want to use. I also liked that they came in #10 and #7 which I found to be ideal sizes for my N scale track plan.....DaveB

Re F&M

They don't seem to have an online presence - appear to be marketing via Central Hobbies, which is a great Model Train Shop in Vancouver, and has them for sale online. 

https://www.facebook.com/CentralHobbiesVancouver/posts/new-products-from-fm-models-3d-printed-cpr-high-level-switch-stands-in-ho-and-n-/5259604740746831/

F&M has some very cool stuff. I think they generally make everything in all of HO, TT and N.

I've managed to misplace my switch stands in a pile of train parts, but re the low profile, I think you could just leave the indicator off, or perhaps write to them (address below) with photos of what you want - they seem to be really good at CAD and 3D Printing.

Wheel Stops

And this beautiful snow plow (N Scale).

Here's a really crappy picture of it on Central Hobbies' WONDERFUL N Scale window display layout.  I wish I could get a track plan for it.  I'd build it and keep just enough N Scale to run on that or build it and give it to me new Grandson when he's old enough.  Incidentally, this layout is done entirely with code 55, so they might also have ideas re your turnouts.  The lady there is a very active modeler and built the plow. and the switchstand.

or I guess you could write to them.

Or there are these from Rapido...

http://www.ovrtrains.com/Rapido-320104-HO-RailCrew-Switch-Stand-1-pcs.html

Or the ever reliable caboose hobbies ground throws.  

hole location

The hole in the benchwork doesn't have to be directly below whatever hole in the tie you use, you can have a wire that goes down through the tie, immediately bends 90 degrees and runs along the top of the benchwork (in line with the throwbar) and then bends 90 degrees again to plunge through the benchwork to the tortoise mounted underneath, well off to the side of the track. 

You can hide the wire running across the top of the benchwork with some grass and the big hole with a shrub. Or you can run the horizontal portion through a tube and completely bury the tube under landscape material. 

Took some pictures of short switch stands today ...

... one of my favourite train spotting spots in New West. 

ll this is top help in using the pre-drilled holes in the tie bar from a position off to the side of the turnout.

Same stand, different target

Hey, that ain’t no switchstand.  But there was one behind him before he jumped in front of the camera!
 

Atlas Code 55 Turnouts

I'm currently dealing with the same problem myself. What I've chosen to do is use tortoise remotes. Doing this does cost more and takes more work under the table but the result is that the throw wire pivots to move the throw bar rather than "slide" it. The pivot point can be set off to the side of the track in line with the hole of the throw bar. One other thing that I'm doing is instead of following the remote's instructions to bend the throw wire over the top of the ties and then 90 degrees into the throw bar hole is to bend the throw wire over the track bed and then up through the hole in the throw bar. This helps hide the wire a little more. I've not done any ballasting yet so that may be something I'll have to deal with later on. I suggest that you might want to  go on the vendor's website to look at instructions for the tortoise remote to see if this idea might work for you.