I think the behavior you describe is the right one since we're talking about breakpoints set in a specific file and at a given line. Eclipse always tries to install all breakpoints listed in Breakpoints view in a new debug session. Any BP set in a file and on a given line, will have associated some properties, and amongst them there's the absolute file path. See the following screenshots.


So, the breakpoints are actually linked to a project by very simple means - file path and project location.
When you have two breakpoints like the ones below, set in two different projects, Eclipse will attempt to install both of them when starting a debug session on any project. However, only some of the breakpoints will be resolved based on the debug information found inside the elf files. Basically, if you'll inspect the debug dump (obtained with readelf), you'll see something like:
<e9d> DW_AT_name : (indirect string, offset: 0x117a): ../source/frdmkl26z_hello_world.c
<ea1> DW_AT_comp_dir : (indirect string, offset: 0x52f): C:\SomeFolder\MCUXpressoIDE_11.0.1_2563\workspace.5\frdmkl26z_demo_apps_hello_world_1\Debug
Based on the actual location of the source file on the host computer and based on the two descriptors found in the DWARF information, GDB decides whether a breakpoint can be installed or not in a given context. If breakpoint cannot be resolved, we'll see it being marked as pending:
info breakpoints
Num Type Disp Enb Address What
1 breakpoint keep y <PENDING> C:\\SomeFolder\\MCUXpressoIDE_11.0.1_2563\\workspace.5\\frdmk64f_hello_world_1\\source\\frdm64f_hello_world.c:37
3 breakpoint keep y 0x0000050e in main at ../source/frdmkl26z_hello_world.c:60
There's a filtering option available in Eclipse but this needs to be configured at debug time. This way, you can limit a given breakpoint to a given target but the configuration is not persistent for subsequent debug sessions.

Given the above mentioned comments, are there any side effects of current behavior in your use case? What isn't working in fact? It's not very clear from your description.
Greetings,
MCUXpresso IDE Support