Too many licenses identified and different result single file vs project

### Description

Two problems:
1. Different result when scanning single file compared to an entire project. This issue seems to be partly related to: #3523
2. GPLv3 and other licenses seem to be incorrectly identified but ignored? Partly relates to the 3523 as well.

### How To Reproduce

> Tell us how to reproduce the issue.

Execute attached file (freetype.sh) to download project and single file, scan and present data from them separately.

**Problem (1)**
See output from script. The licenses detected are as follows:
* Scanning single file, `t1afm.c`, gives: `freetype`
* Scanning entire gives (for the same file, `t1afm.c`): `mit AND public-domain AND gpl-2.0 AND freetype`

**Problem (2)**
See output from script.

A *GPLv3* rule is matched.
```
Expression:freetype OR gpl-3.0
RULE:https://github.com/nexB/scancode-toolkit/tree/develop/src/licensedcode/data/rules/freetype_or_gpl-3.0_1.RULE
```
I guess this is **incorrectly identified** by the following text in `freetype-2.13.2/LICENSE.TXT`:
```
Note that this license is compatible to the GNU General Public
License version 3, but not version 2.
```

The below, I think, relates to #3523
```
Expression:mit
RULE:https://github.com/nexB/scancode-toolkit/tree/develop/src/licensedcode/data/rules/mit_14.RULE
```
I think this is caused by the top level license as found in `freetype-2.13.2/LICENSE.TXT`. Not valid for the file `t1afm.c`

```
Expression:public-domain
RULE:https://github.com/nexB/scancode-toolkit/tree/develop/src/licensedcode/data/rules/public-domain_285.RULE
```
I think this is caused by the top level license as found in `freetype-2.13.2/LICENSE.TXT`. Not valid for the file `t1afm.c`

```
Expression:gpl-2.0
RULE:https://github.com/nexB/scancode-toolkit/tree/develop/src/licensedcode/data/rules/gpl-2.0_1022.RULE

Expression:freetype
RULE:https://github.com/nexB/scancode-toolkit/tree/develop/src/licensedcode/data/licenses/freetype.LICENSE
```
Both are oK.

### System configuration

> For bug reports, it really helps us to know:

* What OS are you running on? (Windows/MacOS/Linux)
```
$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 22.04.3 LTS
Release: 22.04
Codename: jammy
```
* What version of scancode-toolkit was used to generate the scan file?
```
$ scancode --version
ScanCode version: 32.0.8
ScanCode Output Format version: 3.0.0
SPDX License list version: 3.21
```
* What installation method was used to install/run scancode? (pip/source download/other)
pip

... thanks for all your work on Scancode :)