So this being a discussion forum...
Let's take as a given that Scaletrax switches "weld" the outer-rails together which for sake of discussion means you can't have a switch section be part of an insulated-rail trigger section. To be clear, this is a premise of the following ramblings:
Backing up a bit, this is the "classic" occupancy detection problem where you can't place enough sensors to fully span/cover the length of rail of interest. The insulated-rail method is so simple and inexpensive as to be elegant! But if that's not in the cards, here are 2 ideas for consideration.
Method 1) From the HO or 2-rail world, one approach to occupancy detection is to detect center-rail power consumption in a block. A block can include switches. Power consumption is via a current-sensor which triggers when the block current exceeds some threshold...say, 0.1 Amps. This method typically means placing a powered caboose (or whatever) at the end of the consist. The 2-rail guys know about the special 2-rail wheel axles that have embedded resistor that draws power and can be placed in unpowered cars.
This is of course just a half-baked idea. Even with off-the-shelf current-detection modules there is homework to be done.
Method 2) From the 2-rail (and 3-rail) world, if impractical to install a detection method that spans the entire trigger section, then point-of-detection sensor can be augmented with a timer to extend the trigger. It's not fool-proof of course but can work in many applications. For example, optical detectors like the Lionel 153IR or MTH ITAD detect occupancy at one point and then extend the trigger output electronically to simulate occupancy detection over some length of track beyond the sensor. Multiple sensors can be tied together to cover a wider span; the classic example of this is a sensor on both sides of a grade crossing to trigger the signal from either train direction and to hold the signal active until the train exits the other side.
So for the matter at hand, the switches would have to be isolated from the insulated trigger sections with additional cuts/gaps. Then multiple trigger islands would be tied together. For the special case of running a short-consist or a lone switcher engine that could completely reside on just a switch section, a timer can extend the trigger by, say, 5 seconds to allow the consist to reach the next island without the trigger momentarily disappearing.
Like method 1, this is a half-baked idea. One thing going for this method is the existing setup already uses 12V DC relay modules and there is a source of 12V DC. There are many inexpensive 12V timer modules that could be enlisted to provide a settable time-delay to extend the trigger duration. For example, from eBay or Amazon:
Or a DIY'er comfortable working at the component level could cobble together a 12V DC trigger extender for less than 50 cents using a handful of garden-variety parts (resistors, capacitors, diodes).