when you have the new route in the box with the route you are merging, you can use the left / right Cursor (arrow) keys to rotate it in either direction, do note though, that you have to line it up squarely!! or you can put it at an angle. you cannot (or I haven't figured it out yet) rotate the route you start from, only the route you are merging with that route. If you want the other route rotated, start with the route you want fixed in position.
try it and you will see what I mean
This has always been the case and has been asked for ages ago, but there are technical reasons why it can't be done.
The solution is to build 'tween boards, meaning a couple of boards or more to align the tracks where you want them.
In case you ask, you can't raise or lower the heights either in game. This can be done, however, using TransDEM with mixed results whether it will work or not depending upon the route.