The LDraw Boxer project is licensed under the GPLv2 which allows you to modify the code to make your own variation, as you want to do.
The Free Pascal compiler is a program that reads the source code and generates the binary code that your computer understands. The output of a compiler does not fall under the licensing terms, it is considered your work. The compiler does however link a small runtime library into your program that provides basic functionality needed to make your program work, with Free Pascal this rtl library is licensed under the LGPLv2.1 and as stated after the quote you have shown -
the runtime library (RTL) come under a modified Library GNU Public License (LGPL). This license does not impose any kind of license on the created applications. It is therefore possible to create closed source or proprietary software using the Free Pascal Compiler.
The GPLv2 and LGPLv2.1 are compatible licenses and a project can combine work covered by both. See the GPL compatibility listing here.
So the Free Pascal compiler does not add any licensing restrictions to your project, the use of the LDraw project does and those terms are the one you need to comply with. Note that you can modify, build and use your own version as you wish, the GPL comes into play if you share your modified program with others, they must also get access to your modified code used to build the program.