You have two choices, and I'll try to answer you tree tile question at the bottom. Prepare for a wall of text.
As you suggest, a couple of trees would work but not very elegant. A better solution is to replace the building with a different working building. Same process as adding trees.
I think the real issue here is that no one, so far as I've read, has identified the exact building for Hitech.
All building are available in the OE. If you can identify the offending building shape and pass that along to Hitech, he has the tools to fix the building or replace it with another. You don't even need anything other than a text editor to replace every offending building in the entire terrset, see below.
The terrset tiles use a smaller subset of the building objects but they are not interchangeable. By that I mean the same building in a terrset is a speedtree object and that isn't the same as it's match in an object tile, think airfield, building.
Open the OE, under the Shapes drop-down menu, select any object, then type 'b' to jump to the b's for building. Scroll through the list to the matching bld# or possibly, in the facbld# shapes. Pass the offending shape name to Hitech.
For the benefit of others reading this...
So, in the OE, you can build object tiles such as Airfields and Cities. The OE is set for building object tiles by default (New). The OE comes with pre-built objects. The individual objects themselves are built with AC3D and you can create new stand alone AC3D objects, see the towers in Monday Night Madness. Jaeger dropped those towers into his terrains as independent items.
For the benefit of Special Events terrain builders, ground tiles for cities, fields, etc., require the additions of several grayscale bitmaps to establish things like plants and grass (one bitmap) and gravel and mud (a different bitmap). In addition, the ground, say for a 1 mile x 1 mile tile, is supposed to be broken up into smaller collision areas, inspect the tile under a small airfield (use Edit Tree or export [TE?] and open the object in a text editor.) iirc, there are 64 individual 660' x 660' square pieces, and they are all flat making it one of the easiest tiles to decipher and learn. Once you have the ground tile built, with it's RGB color bitmap, the normal _n bitmap, the ground grayscale and the detail grayscale, load it into the OE to add your buildings. Now you have a nice tile with buildings, grass, dirt road or whatever but NO trees! At that point you need to convince the OE to add trees. iirc, Open Terrset starts the process in the OE but you need to save and reopen the tile first. Once the OE drops into tree mode, you place your trees on your new airfield and it builds the text files the OE turns into speedtree files for your new creation. iirc, you must have an object tile or terrset tile in the OE before you can place any trees. Makes sense you need something for a base but not sure as it's been five years since I tried that.
Edit: You can export the airfield ground, rename it and use it for you flat object project. Just replace the bitmaps and add the new objects and trees you want.
For custom terrain tiles, you don't need the 1m x 1m ground, all are basically exactly like the flat airfield tile from above. Terrset tiles are all 1m x 1m and made of those 64 sub-squares. At this time, the 4 large terrset tiles use a 1024 x 1024 bitmap set while the smaller tiles use a 512 x 512 bitmap sets, unfortunately. Trying to create small tiles with nice roads or paths make giant wide turnpikes, 5280' / 508 pixels = 10.3' squares in the terrain and 2 pixel wide roads don't look good. You can use anti-aliasing for the RGB but not the grayscales that determine the ground/vegitation type. I've been told the sizes are restricted due to players with less capable hardware. imho the game would look much better with 2024 & 1024 bitmaps but that's for another discussion.
You asked about placing trees at the offending building. Turns out it's been too long since I worked with terrsets to remember details but Hitech posted the zip files for most of the terrsets in the Beta forum long ago.
Find the latest one, of a couple available, and extract the files, then move the folder(s) to your C:\Hitech Creations\Aces High III\ah3terr\ folder
Launch the OE, File, Open Terrain Tile, select one of the terrain types terrset## (ETO), then spdtree folder, then swa folder, and select a tile, i.e. mgrass.
The OE does not need to load a ground tile for any terrset type, it loads the mgrass texture as flat and populates it with the speedtree trees and objects from the swa text file. From there you can modify the tile.
(C:\Hitech Creations\Aces High III\ah3terr\terrset00\spdtree\swa)
If you use windows file explorer, and go to the swa folder, you'll find a list of (text) swa files with a format something like this:
a spdtree Folder you can ignore
decidforest.swa
drygrass.swa
etc.
Open one of the .swa files with notepad.
The format is line-based:
"../Trees/Tree type.srt"
number of trees
location, rotation, scale, etc for each of number of trees
This is a sample I pulled randomly with two trees in it.
"../Trees/LondonPlaneSpec.srt"
2
1064.13 -1075.15 20 0 0 1 -0.141294 -0.989968 0 1
-77.84 -1371.32 20 0 0 1 0.800313 0.599583 0 1
Most of these tree types are very large and include the speedtree buildings but you can see, that by changing the tree type, you change all those listed speedtree objects in one fell swoop.
Save your new source file and reopen to see the change
Rebuild the res file and you're done. Except for getting it included in an update to every players game files.
The "Open Beta Test" board contains loads of information on this and other subjects dealing with terrain building and tile modification. Anyone wishing to use the OE should start there.