The parameter_overrides field in [default.deploy.parameters] consists of space-separated Key=Value pairs. While toml supports multiline strings, it causes an error because it does not process newlines as whitespace. Fixing that would be an improvement, but what I'd really prefer is that these key-value pairs get their own proper section. Say my samconfig.toml would look like:

version=0.1
[default.deploy.parameters]
stack_name = "my-app-stack"
s3_bucket = "my-source-bucket"

[default.deploy.parameters.template_parameters]
TemplateInput1 = "Value1"
TemplateInput2 = "Value2"

equivalent to

version=0.1
[default.deploy.parameters]
stack_name = "my-app-stack"
s3_bucket = "my-source-bucket"
parameter_overrides = "TemplateInput1=Value1 TemplateInput2=Value2"

One of the things this would make easier is updating the values in this file programmatically.