By top tube bag, you probably mean a bag that straps to the top of the top tube and the stem, sometimes called a bento box. Those can prevent you from sitting on your top tube at a light, or hit your legs when standing.
David posted a saddle bag that has a bit of stand off distance from your post. Most saddle bags don't do that, but there may be some others that do. A low-profile saddlebag may also work. The one below is made for Ornot (link to the Instagram post) by Rickshaw Bags (link to their product page, may not be permanent).
Bags that mount under the top tube are a possibility. There are bags that fit under the whole top tube, which I think are usually called half frame bags (because they don't fill your entire front triangle). There are a few bags that fit in the front of the bike between the top, head, and down tube intersection like this one from Apidura:
I'm not sure what the standard term is for this. They're less common than half frame bags. But Apidura isn't the only company that makes them.
If you had a Specialized saddle, it has a standardized pair of accessory mounting bolts. Specialized makes a tool kit that mounts to those bolts. Or Lezyne (and probably others) make either bottle cages or adapters with slots for tools - although they won't have room for a tube. You could carry the tube in your jersey pocket or use something like a Voile strap to secure one to your frame. Or you could get a small wallet to carry your entire flat kit. Rapha makes two sizes, although the small version won't easily fit a phone plus a tube and multitool.
Last, you may be thinking of rack-mounted, larger handlebar bags used in bike touring. Lower-profile bags that use straps are available and, in my observation, becoming more fashionable these days. It may be worth reconsidering.
Here's the bag in place with new saddle. it is a little cramped for space, but tools and spare tube fit. Thanks for all the suggestions!
